supporting information - pnas.org · 50 68049 68345 296 glutamyl-trna ... 93 120209 120111 98...

Supporting InformationJager et al. 10.1073/pnas.0909051106

Fig. S1. Basal promoter elements identified upstream of the primary transcripts. The upstream sequences (�40 to -20) of each primary transcript identifiedby cDNA sequencing were aligned using the ClustalW multiple alignment tool (1). After hand correcting the alignment the consensus was visualized withWebLogo (2). The BRE and TATA-box are indicated.

1. Larkin MA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948.2. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: A sequence logo generator. Genome Res 14:1188–1190.

Jager et al. www.pnas.org/cgi/content/short/0909051106 1 of 32

http://www.pnas.org/cgi/content/short/0909051106

Table S1. Comparison of previously experimentally mapped transcriptional start sites with the pyrosequencing results of the cDNAs

ORF no. (1) Gene function (1) Method used Refs. 454-data

MM0719 nifH 5’-RACE Ehlers et al., 2002 (2) n. o.MM0732 glnK1 5’-RACE Ehlers et al., 2002 (3) IdenticalMM0964 glnA1 5’-RACE Veit et al., 2006 (4) IdenticalMM2169 vhtG Primer extension Deppenmeier et al., 1995 (5) IdenticalMM2314 vhoG Primer extension Deppenmeier et al., 1995 (5) n.o.MM2440 Conserved protein 5’-RACE Veit et al., 2006 (4) n.o.Not annotated (2) Located between

MM2503 and MM2504Hypothetical protein Primer extension Conway De Macario et al., 1995 (6) n.o.

MM2504 dnaJ Primer extension Clarens et al., 1995 (7) n.o.MM2505 dnaK Primer extension Clarens et al., 1995 (7) n.o.MM2506 grpE Primer extension Conway De Macario et al., 1995 (6) IdenticalMM3334 mtmC2 5’-RACE Veit et al., 2006 (4) n.o.

n.o., no cDNA obtained.

1. Deppenmeier U, et al. (2002) The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461.2. Ehlers C, Veit K, Gottschalk G, Schmitz RA (2002) Functional organization of a single nif cluster in the mesophilic archaeon Methanosarcina mazei strain Gö1. Archaea 1:143–150.3. Ehlers C, Grabbe R, Veit K, Schmitz RA (2002) Characterization of GlnK1 from Methanosarcina mazei strain Go1: complementation of an Escherichia coli glnK mutant strain by GlnK1.

Journal of bacteriology 184(4):1028–1040.4. Veit K, et al. (2006) Global transcriptional analysis of Methanosarcina mazei strain Gö1 under different nitrogen availabilities. Mol Genet Genomics 276:41–55.5. Deppenmeier U, Blaut M, Lentes S, Herzberg C, Gottschalk G (1995) Analysis of the vhoGAC and vhtGAC operons from Methanosarcina mazei strain Go1, both encoding a

membrane-bound hydrogenase and a cytochrome b. (Translated from eng) Eur J Biochem 227(1–2):261–269 (in eng).6. Conway De Macario E, Clarens M, Macario AJ (1995) Archaeal grpE: Transcription in two different morphologic stages of Methanosarcina mazei and comparison with dnaK and dnaJ.

J Bacteriol 177:544–550.7. Clarens M, Macario AJ, Conway de Macario E (1995) The archaeal dnaK-dnaJ gene cluster: organization and expression in the methanogen Methanosarcina mazei. (Translated from

eng) Journal of molecular biology 250(2):191–201 (in eng).



Table S2. Newly identified ORFs located within intergenic regions (IGRs) in the original genome annotation (1)

Strand ORF no. IGR Function of adjacent genes (2) 5’ end 3’ end size �N score �N score

TATA

box BRE

Sequence

conservation

� 3372 MM�0015/16 Putative methyltransferase/Translation

initiation factor 1A (EIF-1A)

17483 17859 376 15.00 5.00 x x MB

� 3373 MM�0015/16 Putative methyltransferase/Translation

initiation factor 1A (EIF-1A)

18203 18365 162 0.35 — — — MB

� 3374 MM�0039/40 Carbamoyl-phosphate synthase small

chain /Glycine betaine transporter,

ATP-binding protein (OtaA)

50714 50806 92 0.14 0.25 x x —

� 3375 MM�0046/47 Hypothetical protein /Acetylornithine

aminotransferase

61498 61380 118 0.19 0.19 — — MA, MB

� 3376 MM�0117/18 Hypothetical protein /CTP synthase 146454 146150 304 1.60 0.70 x x MA, MB

� 3377 MM�0131/32 Conserved protein /Conserved protein 164001 163800 201 0.14 — x x MA, MB

� 3378 MM�0151/52 Conserved protein /DNA

integration/recombination/invertion

protein

191211 191336 125 0.23 — — — —

� 3379 MM�0587/88 Conserved protein /Conserved protein 718827 718940 113 0.10 0.12 — — —

� 3380 MM�0827/28 Conserved protein /Conserved protein 978565 979041 476 0.21 - x x MA, MB

� 3381 MM�0873/74 Conserved protein /Conserved protein 1032591 1032518 73 0.26 0.55 x x MA, MB

� 3382 MM�0954/55 Hypothetical protein /ABC transporter,

permease protein

1133587 1133930 343 0.21 - x x MA

� 3383 MM�1032/33 Conserved protein /Ferrous iron

transport protein B

1208988 1208683 305 0.38 0.55 x x MA, MB

� 3384 MM�1052/53 Conserved protein /Putative Sensory

protein

1231924 1231741 183 0.11 0.13 — — MA, MB

� 3385 MM�1295/96 DNA primase /NADH oxidase 1539938 1539791 147 0.77 0.68 — — MA, MB

� 3386 MM�1456/57 Universal stress protein /Conserved

protein

1737404 1737763 359 0.10 0.20 x x MA, MB

� 3387 MM�1563/64 Tungsten transporter, ATP binding

protein /Molybdenum

formylmethanofuran dehydrogenase,

subunit

1863835 1863592 243 0.50 0.90 x — MA, MB

� 3388 MM�1599/1600 Integral membrane protein

/Hypothetical protein

1902912 1903247 335 0.70 — x x MA, MB

� 3389 MM�1622/23 Conserved protein /Transposase

(N-terminal domain)

1935089 1934887 202 6.00 2.20 x x MA, MB

� 3390 MM�1661/62 Type I restriction-modification system

restriction subunit /Transcriptional

regulator, ASNC family

1988778 1989459 681 6.10 1.20 x x MA, MB

� 3391 MM�1838/39 Ferredoxin /Conserved protein 2190331 2190138 193 0.14 0.13 x x MA, MB

� 3392 MM�2016/17 HesB protein /Conserved protein 2407162 2407266 104 0.16 0.18 x x MA

� 3393 MM�2024/25 Conserved protein /Hypothetical protein 2417287 2417534 247 0.13 0.30 x x —

� 3394 MM�2208/09 Putative sugar kinase /Conserved protein 2624069 2624291 222 0.13 — x x —

� 3395 MM�2224/25 Trp repressor binding protein

/Glucoamylase

2651657 2651371 286 0.46 — x x MA, MB

� 3396 MM�2391/92 Hypothetical protein

/Long-chain-fatty-acid-CoA ligase

2852631 2853220 589 0.65 0.29 x x MA, MB

� 3397 MM�2414/15 Hypothetical protein /Hypothetical

protein

2875200 2875358 158 0.32 — x — —

� 3398 MM�2434/35 Conserved protein /Hypothetical sensory

transduction histidine kinase

2905386 2905476 90 0.12 0.12 x x —

� 3399 MM�2468/69 Metallo cofactor biosynthesis protein

(moaA/ nifB /pqqE family /Hypothetical

protein

2942178 2942274 96 — 0.12 x — —

� 3401 MM�2519/20 GTP-binding protein homolog

/Conserved protein

3007500 3007806 306 0.10 — x — MA, MB

� 3402 MM�2626/27 DNA-directed RNA polymerase subunit P

/Conserved protein

3128268 3128321 53 — 0.12 — — MA

� 3403 MM�2670/71 Hypothetical protein /Hypothetical

protein

3194148 3194224 76 — 0.12 — — —

� 3404 MM�2753/54 Hypothetical protein /Conserved protein 3300481 3300269 212 1.10 0.24 x x —

� 3405 MM�2767/68 Hypothetical protein /Conserved protein 3318384 3318605 221 0.72 0.18 x x —

� 3406 MM�2781/82 Conserved protein /Glyceraldehyde

3-phosphate dehydrogenase

3335130 3335303 173 0.13 0.58 x x MA, MB

� 3407 MM�2897/98 Pirin /Conserved protein 3480554 3480211 343 0.92 0.18 x — MA



Strand ORF no. IGR Function of adjacent genes (2) 5’ end 3’ end size �N score �N score

TATA

box BRE

Sequence

conservation

� 3408 MM�2927/28 Heteropolysaccharide repeat unit export

protein /Hypothetical protein

3523131 3522902 229 1.10 0.50 x x MA, MB

� 3409 MM�2931/32 Hydrolase /Conserved protein 3528230 3528406 176 1.00 0.24 x — MA, MB

� 3410 MM�3164/65 Conserved protein /Hypothetical protein 3847548 3847731 183 0.14 — x — —

� 3411 MM�3195/96 Transcriptional regulator, MarR family


3884264 3884406 142 0.43 0.55 — — —

� 3412 MM�3246/47 Transposase (N-terminal domain)

/Conserved protein

3946330 3946354 24 — 0.12 — — —

� 3413 MM�3287/88 Hypothetical protein /Conserved protein 3999257 3999480 223 — 0.60 x x —

� 3414 MM�3327/28 Ferredoxin /Conserved protein 4055568 4055740 172 0.16 — — — —

The score indicates the relative clone number per nucleotide within the enriched libraries. MB, M. barkeri; MA, M. acetivorans.

1. Deppenmeier U, et al. (2002) The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461.



Table S3. mRNAs identified to contain long 5’-UTRs

StrandORF

no. (1)

Annotatedtranslational

start (1)

Transcriptionalstart site

(this work)5’-UTR

(nt) Gene function (1) �N score �N scoreTATAbox BRE

� 1 522 302 220 Dipeptide ABC transporter, bindingprotein

0.1 0.08 x x

� 2 2677 2423 254 Dipeptide ABC transporter, bindingprotein

0.1 — x x

� 10 11299 11735 436 Hypothetical protein 0.14 — — —� 11 12748 12378 370 Conserved protein 0.22 0.2 x x� 18 21863 21816 47 Conserved protein — 0.14 x x� 21 25929 25881 48 Conserved protein 0.37 — x —� 40 51425 50989 436 Glycine betaine transporter, ATP-binding

protein (OtaA)0.13 0.11 x x

� 45 59399 59379 20 Hypothetical protein — 0.12 — —� 49 65484 65759 275 Conserved protein 0.27 0.62 x —� 50 68049 68345 296 Glutamyl-tRNA (Gln) amidotransferase 0.18 — x x� 72 98158 98241 83 Thermosome beta-subunit 0.24 0.32 x x� 78 104409 104896 487 Xanthine-guanine

phosphoribosyltransferase— 0.13 x —

� 85 110974 111265 291 Conserved protein 1.8 1.4 x —� 87 113532 113554 22 Pyrimidine-nucleoside phosphorylase — 0.19 — —� 89 115342 115736 394 Hypothetical protein 0.87 1.1 x x� 93 120209 120111 98 Cobyric acid synthase CbiP 0.13 0.12 x x� 97 126740 126884 144 Ornithine cyclodeaminase 0.14 — — —� 118 148154 148278 124 CTP synthase 0.12 — x —� 125 155445 155296 149 Universal stress protein 0.1 — — —� 128 160753 161078 325 ATP-dependent protease La 0.46 0.29 x x� 137 171646 171432 214 Conserved protein 0.14 — — —� 138 173136 173450 314 Conserved protein 0.14 0.19 x x� 144 178642 178470 172 Phosphoribosylamine–glycine ligase 0.4 0.4 — —� 159 206782 206478 304 Hypothetical protein 0.28 — x x� 174 238003 237810 193 Methanol corrinoid protein MtaC3 0.22 — x x� 176 241545 241809 264 Methylcobalamin:coenzyme M

methyltransferase MtaA20.23 — x x

� 178 243509 243117 392 Conserved protein 0.11 — x x� 184 257650 257995 345 SSU ribosomal protein S3AE 0.6 0.37 x x� 190 261351 261176 175 DNA helicase II — 0.45 x x� 198 276738 276764 26 ATP-dependent DNA helicase 0.2 — x x� 205 281636 281336 300 Conserved protein 0.15 — — —� 220 300226 300248 22 Conserved protein 0.35 — x —� 227 307464 307565 101 Conserved protein 0.17 — x x� 230 309343 309297 46 Sodium-calcium exchanger 0.2 — x x� 241 324674 324837 163 Potential ferredoxin oxidoreductase 0.17 — x x� 245 327597 327625 28 Riboflavin synthase, subunit alpha — 0.13 x x� 247 329723 329761 38 Putative inosine monophosphate

dehydrogenase0.17 — x x

� 252 335565 335688 123 Conserved protein 0.14 — x x� 254 339782 339749 33 N5-Methyl-H4MPT:Coenzyme M

Methyltransferase, Subunit X0.1 — x x

� 258 343393 343337 56 Transposase — 0.2 — —� 259 347013 347101 88 Dihydroxy-acid dehydratase 0.14 0.13 x —� 278 374105 374161 56 DNA-cytosine methyltransferase 1 0.44 x —� 285 385388 385571 183 Conserved protein 0.7 0.81 x x� 286 386031 385993 38 Hypothetical protein 0.1 0.25 x x� 288 388062 388045 17 Transcriptional regulator, ArsR family 0.19 — x x� 298 399152 399307 155 Glycine betaine-binding protein — 0.13 x x� 304 407340 407306 34 AAA family ATPase 0.12 0.5 x x� 305 408712 408653 59 Conserved protein 0.13 0.6 x —� 306 410159 410249 90 Metal-dependent hydrolases 0.19 — x —� 313 417424 417354 70 Hypothetical protein 0.11 — x x� 339 447635 447531 104 Putative snRNP Sm-like protein 0.13 0.18 x x� 340 447995 447885 110 LSU ribosomal protein L37E 0.3 0.12 x x� 344 452906 453225 319 Probable cation efflux pump 0.27 0.13 x x� 346 453825 454056 231 Transcriptional regulator, MarR family 0.16 — x x� 351 458507 458427 80 Conserved protein 4.5 — x x



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 355 462606 462789 183 Transposase — 0.13 — —� 356 462764 462533 231 Conserved protein 1 0.3 x x� 362 469092 468869 223 Sulfite reductase, assimilatory-type 0.13 — x —� 386 495643 495892 249 Hypothetical protein 0.32 0.19 x x� 387 496300 496081 219 Heterodisulfate reductase, subunit HdrA 0.7 — — —� 392 504926 504532 394 Hypothetical protein similar to

C-terminal domain of HdrB— 0.12 x x

� 395 508689 508847 158 Surface layer protein (putative) 0.53 0.32 — —� 398 511763 511966 203 Conserved protein — 0.55 x x� 402 515348 515483 135 Conserved protein — 0.44 — —� 403 515777 515653 124 Hypothetical protein similar to

C-terminal domain of HdrB— 0.35 x x

� 408 520378 520501 123 Hypothetical protein 0.11 — x —� 423 537590 537626 36 Conserved protein 0.41 0.13 x x� 436 556320 556528 208 Thioredoxin 0.45 0.1 x x� 440 560659 561129 470 Dihydropteroate synthase 0.3 0.19 x x� 445 565888 565673 215 Hypothetical protein 1.1 3 — —� 452 574937 575307 370 Hypothetical protein 0.11 — x x� 453 575694 575489 205 Conserved protein 1.1 0.35 x —� 456 578207 578224 17 Hydrolase (HAD superfamily) — 0.12 — —� 465 586254 586299 45 Cobalamin biosynthesis protein CbiM 0.65 0.31 x x� 467 590585 590741 156 Conserved protein 0.14 — — —� 479 603626 603724 98 Conserved protein 0.14 — x x� 483 606785 606401 384 Small heat shock protein 0.34 0.7 x x� 485 609742 609828 86 Phosphoglycerate kinase — 0.25 x x� 496 618489 618516 27 Phosphate acetyltransferase 0.11 — x x� 516 643222 643305 83 Hypothetical protein 0.28 0.25 — —� 517 643641 643820 179 Conserved protein 0.1 — — —� 526 654420 654869 449 Hypothetical protein 0.36 — x x� 530 659609 660022 413 Amino acid permease 0.63 0.94 x —� 536 667063 667349 286 Hypothetical protein — 0.13 x x� 545 674599 674553 46 Hypothetical protein — 0.13 x x� 578 705393 705454 61 Phosphate-binding protein 0.14 — x x� 582 710372 710079 293 Glycosyltransferase — 0.13 x x� 584 712965 712793 172 Conserved protein — 0.12 x —� 585 714201 714140 61 Conserved protein 0.2 — — —� 590 721438 721577 139 Glycerol-1-phosphate dehydrogenase

(putative)— 0.12 x x

� 591 722397 722347 50 Conserved membrane protein — 0.12 x x� 593 724369 724177 192 Conserved protein — 0.12 x x� 610 741532 741557 25 Acetyltransferases — 0.62 x x� 617 748892 748727 165 Conserved protein 0.12 0.13 x x� 628 759801 759930 129 Coenzyme F420-dependent

N5,N10-methylenetetrahydromethanopterin reductase

0.4 0.12 x —

� 629 760739 760420 319 Zinc finger protein 0.11 0.12 x —� 666 799088 799046 42 Putative nickel-responsive regulator

NikR1.3 0.3 x x

� 667 800868 801111 243 Nitroreductase family protein — 0.13 — —� 671 806460 806541 81 2-Isopropylmalate synthase 0.17 0.45 x x� 680 817001 817464 463 Conserved protein 0.12 — x x� 683 818872 819151 279 Hypothetical protein 0.11 — x x� 684 819935 819569 366 CO dehydrogenase/acetyl-CoA synthase,

alpha subunit1.2 1.7 — —

� 694 832393 832292 101 Proteasome, beta subunit 0.17 — x x� 697 836856 836327 529 Cell division protein 0.32 0.42 — —� 704 849409 849380 29 Conserved protein 0.22 — — —� 711 856718 856660 58 Transposase 6.5 6 — —� 714 860242 860013 229 Fructose-bisphosphate aldolase 0.14 0.24 x x� 745 892895 893013 118 Conserved protein 0.33 — x x� 747 895027 894686 341 ATP-dependent RNA helicase 3 1.4 x x� 760 908924 908986 62 Ferredoxin 0.55 0.45 x x� 767 916182 916269 87 Conserved protein 0.25 — x x



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 772 922435 922395 40 Conserved protein — 0.12 x x� 786 939357 939485 128 A1AO H � ATPase, Subunit H 0.22 — x x� 799 954184 954169 15 Hypothetical protein 0.45 — x x� 802 956480 956254 226 SSU ribosomal protein S19E — 0.28 x x� 805 958265 958076 189 LSU ribosomal protein L39E 0.12 — x x� 811 961960 962088 128 Stress-responsive transcriptional

regulator0.24 — x —

� 813 964313 964322 9 Conserved protein — 0.25 — —� 817 968465 968637 172 Pyrroline-5-carboxylate reductase — 0.12 — —� 818 969803 969886 83 Glutamate 5-kinase 0.17 — x x� 819 971284 971540 256 Gamma-glutamyl phosphate reductase 0.11 — x x� 820 972172 971906 266 Conserved protein 0.14 — x x� 823 974188 974145 43 Conserved protein 0.32 0.25 x x� 824 975317 975137 180 Universal stress protein 0.16 0.12 x x� 827 978390 978451 61 Conserved protein — 0.12 x x� 829 979997 980044 47 Conserved protein 0.54 0.48 x —� 837 990527 990239 288 Conserved protein — 0.25 x x� 843 999921 999995 74 Coenzyme F390 synthetase/phenylacetyl-

CoA ligase0.26 0.55 x —

� 854 1009138 1009225 87 Cell division cycle protein 48 homolog — 0.12 x x� 855 1009614 1009349 265 Phosphoribosylamidoimidazole-

succinocarboxamide synthase0.22 — x x

� 858 1012669 1012739 70 Protein translation initiation factor 1(IF-1)

0.38 — x —

� 859 1013221 1013128 93 Conserved protein 0.17 0.4 x x� 866 1024490 1024653 163 Periplasmic serine protease 0.17 — x x� 868 1027713 1027747 34 Adenylate cyclase 1.2 — — —� 874 1032667 1032508 159 Conserved protein — 0.13 — —� 881 1041288 1041322 34 Transposase — 0.36 — —� 887 1046973 1046919 54 Cobalt transport ATP-binding protein

CbiO— 0.16 — —

� 889 1050470 1050636 166 Hypothetical protein 0.33 0.19 x x� 893 1054360 1054140 220 Cobalamin biosynthesis protein CbiM 0.16 — x x� 895 1056185 1056350 165 Endonuclease III — 0.24 x x� 905 1070316 1070267 49 Conserved protein 0.11 — x x� 907 1073738 1073772 34 Hypothetical protein 0.19 — x x� 911 1077662 1077519 143 ABC transporter, ATP-binding protein 0.22 0.12 x x� 918 1084945 1084783 162 4-Carboxymuconolactone decarboxylase 0.25 — x x� 922 1089329 1089108 221 Protein iranslation initiation factor 5A

(IF-5A)0.22 — x x

� 923 1089822 1089746 76 Agmatinase — 0.12 x x� 925 1091553 1091668 115 Conserved protein 0.14 — — —� 928 1094377 1094507 130 Conserved protein — 0.13 x x� 940 1112100 1112031 69 Putative flavodoxin 0.11 — x x� 943 1117122 1116923 199 Geranylgeranylglyceryl diphosphate

synthase0.32 — x x

� 944 1118334 1118229 105 Methyl coenzyme M reductase,component A2 homolog

— 0.13 — —

� 947 1123119 1123230 111 Conserved protein 0.11 — x —� 962 1140845 1140779 66 Conserved protein 0.14 0.42 x x� 964 1142131 1142103 28 Glutamine synthetase 0.22 2 x x� 966 1144225 1143974 251 Glutamate synthase, large chain 0.17 0.26 x x� 977 1158274 1158244 30 F420-dependent NADP reductase — 0.18 x x� 984 1163377 1163430 53 Conserved protein — 0.13 — —� 987 1165792 1165826 34 Conserved protein — 0.12 — —� 988 1166252 1166371 119 Conserved protein 0.65 0.85 x x� 991 1168022 1167866 156 Thiol-disulfide isomerase/thioredoxin 0.28 0.24 — —� 1009 1184237 1183955 282 Protein translocase, subunit SecE 0.21 — x x� 1012 1185755 1185597 158 LSU ribosomal protein L1P 0.28 0.12 x x� 1025 1198363 1198416 53 Thiamine biosynthesis protein 0.17 0.31 x —� 1028 1200980 1201037 57 Transcription initiation factor TFIIB 0.53 1 x x� 1032 1207879 1208006 127 Conserved protein 0.17 0.12 x —� 1035 1212528 1212581 53 Amino-acid acetyltransferase 0.2 0.11 x x



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 1051 1230382 1230410 28 Chromosomal protein MC1 1.4 0.3 x x� 1054 1235168 1234919 249 Surface layer protein (putative) 0.16 — x —� 1059 1242273 1242059 214 Formate hydrogenlyase subunit 3 0.11 — x x� 1070 1255824 1255563 261 Methylcobalamin:coenzyme M

methyltransferase MtaA10.7 0.3 x x

� 1073 1262243 1261879 364 Methanol corrinoid protein MtaC2 0.85 0.18 — —� 1081 1273541 1273599 58 Conserved protein 0.38 0.12 x x� 1085 1277375 1277111 264 Conserved protein 0.14 — — —� 1107 1301538 1301756 218 Putative phosphoserine phosphatase 0.16 0.36 — —� 1108 1301932 1301866 66 F420-dependent

methylenetetrahydromethanopterindehydrogenase

0.33 0.5 x x

� 1111 1304292 1304252 40 Thymidylate kinase 0.11 — x x� 1116 1309862 1310274 412 Hypothetical protein — 0.26 x x� 1120 1318036 1318021 15 Conserved protein — 0.19 x —� 1121 1321992 1322166 174 Glycosyl transferase 0.22 0.18 x —� 1122 1323227 1322985 242 Oxidoreductase (hypothetical) 0.13 — x x� 1130 1334146 1334251 105 Hypothetical protein 0.38 0.62 x —� 1132 1335013 1334885 128 UDP-glucose 6-dehydrogenase — 0.13 x x� 1138 1346281 1346243 38 Glycosyl transferase 1.2 0.9 x —� 1140 1350005 1350252 247 Dolichyl-phosphate mannose synthase

related protein0.19 — x x

� 1146 1362756 1362863 107 Conserved protein 0.11 — x x� 1148 1364934 1364666 268 Conserved protein 0.11 — x x� 1150 1367197 1367280 83 Conserved protein 0.22 0.24 x —� 1156 1374221 1373887 334 O-antigen translocase 0.12 0.18 x x� 1157 1376323 1376067 256 Conserved protein — 0.13 x x� 1162 1382250 1382636 386 UDP-N-acetylglucosamine 4-epimerase 0.39 0.24 x x� 1165 1384695 1384958 263 Putative glycosyl hydrolase 0.11 — — —� 1187 1411361 1411516 155 Hypothetical protein 0.8 0.12 x x� 1199 1425436 1425186 250 Conserved protein 0.12 — x x� 1200 1426124 1425935 189 SSU ribosomal protein S17E 0.22 — x x� 1217 1442163 1442343 180 ATP-dependent DNA helicase 0.11 — x x� 1218 1443646 1443546 100 GMP synthase �glutamine-hydrolyzing� 0.24 — x x� 1221 1447585 1447617 32 Chromosomal protein MC1 0.6 1.45 x x� 1226 1453229 1453181 48 Glutamyl-tRNA (Gln) amidotransferase,

subunit C0.13 0.42 x x

� 1231 1457723 1457561 162 SAM-dependent methyltransferases 0.13 — — —� 1236 1463250 1463150 100 Protease HTPX — 0.12 — —� 1244 1473096 1473209 113 Methyl-coenzyme M reductase, beta

subunit8.5 3.9 — —

� 1250 1482802 1482915 113 Cation transporter 0.14 — x —� 1254 1489866 1490045 179 Putative heat shock protein 0.32 0.18 x x� 1271 1505915 1505833 82 2-Dehydro-3-desoxyphosphoheptanote

aldolase1.6 — x x

� 1277 1513550 1513946 396 Methyltransferase — 0.12 — —� 1278 1514554 1514626 72 Triosephosphate isomerase 0.11 0.3 — —� 1279 1515783 1515938 155 Orotidine 5’-phosphate decarboxylase

family protein— 0.24 x x

� 1284 1524905 1524894 11 2-Isopropylmalate synthase 1 0.5 x x� 1291 1533847 1533914 67 (S)-2-Hydroxy-acid dehydrogenase 0.22 — x —� 1292 1534111 1533863 248 Archaeosine tRNA-ribosyltransferase 0.1 — x —� 1294 1536846 1536876 30 Conserved protein 0.14 0.63 x x� 1296 1540365 1540125 240 NADH oxidase 0.24 0.61 x x� 1301 1548908 1548669 239 Conserved protein 0.16 — x x� 1313 1562695 1563030 335 UMP/CMP kinase related protein 0.38 0.85 x x� 1321 1575910 1576361 451 Formylmethanofuran–

tetrahydromethanopterinformyltransferase

0.19 — x —

� 1337 1596833 1597142 309 Hypothetical protein — 0.12 — —� 1345 1609877 1609783 94 DNA polymerase II small subunit — 0.18 x —� 1347 1613824 1613401 423 Peptide chain release factor 0.1 — x x� 1355 1624178 1623999 179 Conserved protein 2.8 1 x x



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 1359 1625543 1625446 97 Hypothetical protein — 0.12 x x� 1362 1628725 1628943 218 ABC transporter, periplasmic binding

protein0.24 — x x

� 1364 1633238 1633514 276 S-layer protein 0.16 0.12 x x� 1365 1634425 1634718 293 Thiamin-monophosphate kinase 0.11 — x —� 1368 1638784 1639098 314 Glutaredoxin-like protein 0.18 — — —� 1370 1641408 1641601 193 Myo-inositol-1-phosphate synthase 0.27 0.18 — —� 1371 1641948 1641500 448 Archaeal protein Translation Initiation

Factor 2B subunit 1 (aIF-2B1)— 0.43 x —

� 1372 1643373 1643150 223 Hypothetical protein — 0.13 x x� 1375 1647406 1647026 380 Polyphosphate kinase 0.56 0.75 x —� 1379 1658018 1658070 52 Thermosome, alpha subunit 7.1 2.6 x x� 1385 1665841 1665970 129 Conserved protein 0.9 0.82 x —� 1393 1677174 1677348 174 Molybdenum cofactor biosynthesis

protein A0.14 0.12 — —

� 1394 1677516 1677218 298 Cobyrinic acid a,c-diamide synthase 0.1 0.48 x x� 1397 1681666 1681810 144 DNA polymerase sliding clamp 0.16 0.12 x x� 1402 1684408 1684397 11 Phosphatidylserine decarboxylase 0.14 0.18 x x� 1411 1694174 1694091 83 Hypothetical protein 0.11 — — —� 1414 1696967 1696937 30 Conserved protein 0.11 — x x� 1420 1703524 1703784 260 Hypothetical protein 0.32 0.24 x x� 1421 1703918 1703740 178 Conserved protein — 0.12 x —� 1432 1714337 1714378 41 Hypothetical protein 0.16 0.54 x x� 1438 1719494 1719788 294 Monomethylamine corrinoid protein

MtmC10.32 0.18 x —

� 1440 1721763 1721532 231 Conserved protein 0.13 — x x� 1445 1728981 1729343 362 Lysly-tRNA synthetase (PylS) 4.2 4.2 x x� 1456 1736997 1737168 171 Universal stress protein 0.14 — x x� 1464 1747797 1747972 175 Hypothetical protein 3.6 1.2 — —� 1471 1755719 1755815 96 Tryptophanyl-tRNA synthetase 0.68 0.12 x x� 1476 1759673 1759973 300 LSU ribosomal protein L10E 0.9 0.18 x —� 1485 1769072 1768872 200 Conserved protein — 0.12 x x� 1490 1777043 1777119 76 3-Isopropylmalate dehydratase 0.16 0.18 x x� 1492 1779206 1778927 279 Conserved protein 0.11 — x —� 1493 1781668 1781696 28 Conserved protein 0.11 — x x� 1502 1792087 1792216 129 S-adenosylmethionine synthetase 0.24 — x —� 1503 1792599 1792535 64 ATP phosphoribosyltransferase 0.4 0.12 x x� 1504 1793554 1793531 23 Phosphoribosylformimino-5-

aminoimidazole carboxamide ribotideisomerase

— 0.12 — —

� 1517 1809553 1810040 487 Cysteine desulfurase 0.8 0.1 x x� 1518 1810831 1811057 226 Conserved protein — 0.14 x —� 1521 1812789 1812527 262 Phosphoglucomutase/

phosphomannomutase0.2 — x x

� 1527 1822098 1822221 123 Citrate (si) synthase 0.2 0.36 x x� 1536 1834796 1834692 104 CDP-diacylglycerol–glycerol-3-phosphate

3-phosphatidyltransferase0.16 — x x

� 1547 1844982 1845101 119 TetrahydromethanopterinS-methyltransferase, subunit E

0.22 0.18 — —

� 1550 1849515 1849316 199 putative molybdenum transport proteinModA

0.2 — x x

� 1553 1854922 1855074 152 Transporter, RND superfamily — 0.24 — —� 1557 1857592 1857611 19 Signal recognition particle SEC65

subunit— 0.3 — —

� 1564 1863884 1863542 342 Molybdenum formylmethanofurandehydrogenase, subunit

— 0.18 x x

� 1574 1876045 1876245 200 Conserved protein 0.16 0.42 x x� 1580 1882342 1882372 30 Molybdate-binding protein — 0.12 — —� 1589 1894195 1894390 195 Surface layer protein (putative) 0.78 0.56 — —� 1601 1904236 1903993 243 Cobalamin biosynthesis protein CobN 0.24 — x x� 1602 1909189 1908811 378 Cobalamin biosynthesis protein CobN 0.22 — x x� 1616 1927818 1927507 311 Phosphoribosylaminoimidazole

carboxylase0.27 0.42 — —



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 1619 1931403 1931494 91 Ferredoxin 6 1.4 x x� 1625 1937385 1937522 137 Conserved protein 0.14 — — —� 1631 1945708 1945675 33 Iron-Sulfur Flavoprotein 0.11 — x —� 1642 1957242 1957206 36 Conserved transmembrane protein — 0.16 x —� 1648 1968267 1968506 239 Methanol corrinoid protein MtaC1 0.24 0.5 x —� 1649 1969213 1968986 227 Conserved protein 0.7 0.26 x x� 1681 2019565 2020031 466 CbiD protein — 0.5 x —� 1687 2030838 2030424 414 Dimethylamine corrinoid protein MtbC1 1.1 0.3 x x� 1695 2037622 2037588 34 Conserved protein 0.1 — x —� 1696 2038955 2038604 351 Lysyl-tRNA synthetase, class I 0.26 — x x� 1698 2041542 2041599 57 Conserved protein 0.58 0.12 x —� 1709 2051522 2051474 48 Conserved protein 0.1 — x x� 1711 2053311 2053253 58 Cobalt-zinc-cadmium resistance protein 0.1 — x x� 1713 2055906 2055634 272 Conserved protein 0.26 0.3 x x� 1723 2067511 2067468 43 Conserved protein — 0.13 — —� 1730 2072274 2072036 238 Transposase — 0.12 x x� 1743 2084644 2084332 312 Glutamate-1-semialdehyde

2,1-aminomutase— 0.2 — —

� 1752 2094693 2094449 244 Conserved protein — 0.12 x x� 1755 2098200 2098065 135 LSU ribosomal protein L18E 0.9 0.3 x x� 1771 2115291 2115192 99 Hypothetical protein 0.75 0.85 x x� 1778 2123662 2123734 72 Cobalt-zinc-cadmium resistance protein 0.12 — x —� 1781 2126112 2125725 387 Hypothetical sensory transduction

histidine kinase0.44 0.12 x x

� 1782 2128309 2128230 79 Sodium/glutamate symport carrierprotein

— 0.35 x x

� 1790 2138403 2138305 98 Conserved protein — 0.25 x —� 1793 2140854 2140792 62 Hypothetical protein 0.72 0.18 x —� 1796 2145715 2145915 200 Conserved protein — 0.18 — —� 1802 2151057 2150984 73 Aspartate aminotransferase 0.7 — — —� 1809 2158732 2158976 244 LSU ribosomal protein L44E — 0.26 x —� 1816 2166356 2166263 93 Conserved protein 0.6 0.1 x x� 1824 2174919 2174810 109 Ferredoxin 0.65 0.7 x x� 1825 2175479 2175521 42 DNA binding protein 0.14 — x x� 1836 2188602 2188709 107 Cell division control protein (MCM

family)0.24 — x x

� 1843 2195032 2194886 146 Heterodisulfide reductase, subunit HdrE 0.21 0.42 x x� 1845 2197153 2196974 179 Conserved protein — 0.18 — —� 1851 2201994 2201842 152 Hypothetical protein 0.23 0.24 x —� 1875 2228317 2228206 111 Conserved protein 0.5 — x x� 1876 2230892 2230662 230 Purine phosphoribosyltransferase 0.12 — x —� 1880 2234475 2234337 138 DNA-directed RNA polymerase subunit L 0.21 0.35 x x� 1904 2263194 2263094 100 Hypothetical membrane spanning

protein0.24 0.64 x x

� 1911 2269793 2269663 130 Cysteinyl-tRNA synthetase — 0.12 x x� 1915 2274419 2274267 152 Hypothetical sensory transduction

histidine kinase0.16 — x x

� 1922 2286575 2286710 135 Hypothetical protein 0.3 — x x� 1929 2294319 2294144 175 Hypothetical protein 0.13 0.24 x x� 1931 2298295 2297819 476 Sensory Transduction protein Kinase 0.26 0.12 x x� 1938 2306509 2306408 101 Hypothetical protein 6.4 2.2 x x� 1940 2308958 2308754 204 Glutamine transporter, permease

protein— 0.12 x —

� 1951 2322329 2322413 84 Hypothetical protein 1.6 — x —� 1961 2331071 2331310 239 Hypothetical protein 0.14 0.14 x —� 1966 2336584 2336796 212 Malate dehydrogenase 0.24 — x x� 1968 2338029 2337866 163 Cupin-type phosphoglucose isomerases 0.17 0.5 — —� 1976 2347826 2347659 167 Conserved protein 1.5 0.8 x x� 1985 2364814 2364590 224 Hypothetical protein 0.11 0.18 — —� 1986 2365683 2365597 86 Regulatory protein (putative) 0.11 — x x� 2010 2395923 2395786 137 Phosphate transport system protein 0.11 — — —� 2016 2407032 2407110 78 HesB protein 0.18 1 x x� 2022 2414777 2414679 98 Transporter, LysE family — 0.35 x x



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 2029 2425620 2425574 46 Conserved protein 0.39 0.23 x x� 2033 2430344 2430475 131 Stomatin-like protein 0.44 0.5 x x� 2034 2430902 2430320 582 Conserved protein 0.18 0.18 x —� 2039 2436779 2436538 241 SSU ribosomal protein S8E 1.2 0.7 x x� 2066 2461208 2461031 177 SSU ribosomal protein S15P 0.11 — x x� 2069 2464991 2465400 409 Ferric enterobactin ABC transporter,

solute binding protein (FepB)0.22 0.24 x —

� 2072 2470547 2470256 291 Putative dinucleotide-utilizing enzyme — 0.12 x —� 2073 2471811 2471619 192 Quinolinate synthetase A 0.64 0.47 x x� 2078 2478733 2478437 296 Conserved protein 0.29 — x x� 2096 2501719 2501651 68 UDP-N-acetylglucosamine-1-phosphate

transferase0.44 0.12 x x

� 2115 2528087 2528397 310 Protease HTPX homolog 0.6 0.26 x x� 2118 2531905 2531589 316 Hypothetical protein 0.32 — x x� 2124 2538501 2537839 662 LSU ribosomal protein L3P 0.4 0.7 x x� 2155 2557860 2557772 88 SSU ribosomal protein S13P 0.29 0.18 x x� 2169 2571365 2571278 87 F420-nonreducing hydrogenase II, small

subunit (VhtG)0.29 0.82 x x

� 2174 2577509 2577608 99 Conserved protein — 0.18 x —� 2181 2586726 2586646 80 Fructose-1,6-bisphosphatase 0.3 0.29 x x� 2193 2601848 2601826 22 DNA repair protein (MRE11/RAD32

family)0.13 — x x

� 2209 2624641 2624511 130 Conserved protein 0.16 — x x� 2210 2628924 2629160 236 Oligosaccharyl transferase 0.2 — — —� 2248 2676033 2675974 59 Conserved protein 0.1 — x x� 2264 2690335 2690520 185 Protein translation elongation factor 1A

(EF-1A)0.16 0.12 — —

� 2269 2694803 2694860 57 LSU ribosomal protein L30E 0.28 — x x� 2278 2717212 2717329 117 Adenosylhomocysteinase — 0.32 x —� 2279 2718874 2719005 131 Chlorohydrolase family protein — 0.14 x —� 2289 2728321 2728279 42 Hypothetical protein — 0.12 x x� 2305 2759796 2760108 312 Sodium/proline symporter 0.12 — x —� 2315 2773179 2772761 418 Hydrogenase expression/formation

protein0.1 — x x

� 2326 2784313 2784303 10 COP associated protein — 0.12 x x� 2327 2784704 2784631 73 COP associated protein 0.26 0.12 x x� 2335 2793152 2793043 109 Conserved protein 5 0.18 x x� 2336 2794031 2793526 505 Translation initiation factor 1A (EIF-1A) 0.18 — — —� 2337 2794761 2794650 111 Conserved protein 8.1 — x x� 2338 2795360 2795242 118 Conserved protein in Methanosarcina

spec.0.18 — x x

� 2340 2797986 2798049 63 Acetolactate synthase 0.11 — — —� 2346 2804059 2803980 79 Methyltransferase 0.37 0.23 x x� 2352 2811477 2811429 48 Conserved protein 1.7 0.6 x —� 2363 2819580 2819397 183 Conserved protein 0.12 — x —� 2364 2821477 2821425 52 GTP-binding protein 0.16 — x x� 2369 2825620 2825449 171 Cytochrome c-type biogenesis protein — 0.46 — —� 2370 2827609 2828063 454 GTP-binding protein 0.24 0.3 x —� 2371 2828110 2827880 230 Conserved protein 0.16 0.12 x x� 2381 2840688 2840578 110 Conserved protein 0.11 — — —� 2382 2841298 2841115 183 Hypothetical protein 0.1 — x —� 2383 2841563 2841363 200 Small nuclear riboprotein (snRNA)

homolog1.6 0.3 x x

� 2386 2844698 2844533 165 Hypothetical protein 0.23 0.23 x x� 2394 2856330 2856412 82 Transcriptional regulator, MerR family — 0.32 x x� 2416 2876691 2876555 136 Transcriptional regulator, ASNC family 0.28 0.3 x x� 2419 2881210 2881023 187 DNA gyrase, subunit B 0.18 — — —� 2423 2891414 2891117 297 Superoxide dismutase 0.13 — x —� 2432 2901968 2901823 145 Putative pyridoxine biosynthesis protein 0.22 — x x� 2442 2915444 2915258 186 Conserved protein 0.23 0.23 — —� 2446 2919355 2919017 338 Transcriptional regulator, ArsR family — 0.18 x x� 2449 2921987 2921801 186 Conserved protein — 0.18 x —� 2460 2936059 2936126 67 Dipeptide/oligopeptide-binding protein 0.58 0.12 x x



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 2467 2941130 2941301 171 LSU ribosomal protein L7AE 0.56 0.42 x —� 2491 2969244 2969575 331 F420H2 dehydrogenase, subunitA — 0.12 x —� 2499 2977687 2977473 214 Geranylgeranyl reductase — 0.42 — —� 2506 2989798 2989869 71 GrpE protein 0.22 0.12 x x� 2508 2991856 2992071 215 Heat shock protein 0.14 — — —� 2516 3001574 3001331 243 Probable transcriptional regulator 0.13 — x —� 2531 3017885 3018186 301 Hypothetical protein 0.9 0.12 x x� 2537 3024386 3024195 191 Hypothetical protein 0.19 — x —� 2551 3035713 3035425 288 Acetyltransferase — 0.4 x —� 2556 3039757 3039697 60 ATP-dependent RNA helicase — 0.35 — —� 2557 3041787 3041604 183 Catalase 0.16 0.35 x —� 2582 3071946 3071992 46 Hypothetical protein 0.12 0.26 x x� 2583 3072435 3072560 125 Sec-independent protein translocase,

protein0.12 0.26 x —

� 2596 3093621 3093735 114 Hypothetical protein 0.22 0.12 x x� 2599 3096421 3096099 322 Hypothetical protein 0.7 — x x� 2616 3119379 3119301 78 LSU ribosomal protein L15E 0.18 — x x� 2625 3127741 3127628 113 LSU ribosomal protein L37AE 0.24 0.18 x x� 2634 3140930 3140728 202 2-Keto acid:ferredoxin oxidoreductase

subunit alpha0.1 — x x

� 2640 3151632 3151601 31 Magnesium and cobalt transport proteinCorA

0.11 — x x

� 2653 3169299 3169574 275 N5,N10-methenyltetrahydromethanopterincyclohydrolase

— 0.12 x —

� 2656 3175080 3175481 401 Peptidyl-prolyl cis-trans isomerase 0.14 — x x� 2659 3177337 3177134 203 Acetyltransferase — 0.1 x —� 2681 3205646 3205749 103 Hypothetical protein 0.28 0.18 x x� 2682 3206043 3205729 314 Transposase 0.16 0.18 x x� 2693 3218252 3218200 52 Hypothetical protein 0.13 — x x� 2747 3288741 3288442 299 Hypothetical protein 0.1 0.12 x —� 2748 3290910 3290606 304 Hypothetical sensory transduction

histidine kinase— 0.11 x x

� 2751 3296786 3296991 205 Conserved protein 0.2 — — —� 2752 3298276 3298652 376 Hypothetical protein 0.18 — x x� 2763 3314653 3314469 184 Putative DNA recombinase 0.13 0.18 x x� 2773 3327153 3327319 166 Two component system histidine kinase — 0.2 x —� 2778 3331391 3331465 74 Cobalt-zinc-cadmium resistance protein 0.14 — x —� 2780 3333574 3333527 47 Hypothetical protein — 0.24 — —� 2785 3338845 3338822 23 2-Isopropylmalate synthase 0.18 — x x� 2786 3340890 3341130 240 Conserved protein 0.22 — — —� 2795 3352233 3352121 112 Conserved protein — 0.17 x x� 2798 3357284 3356913 371 Conserved protein 0.29 0.23 x x� 2812 3376311 3376345 34 Phenylalanyl-tRNA synthetase, beta

chain0.14 — — —

� 2828 3392891 3393001 110 Conserved protein 0.18 — x —� 2836 3401314 3401292 22 Enolase 0.1 0.23 — —� 2841 3410114 3410258 144 Acetolactate synthase 0.54 0.18 — —� 2843 3411741 3411618 123 Hypothetical protein 0.29 — x x� 2845 3414977 3415002 25 Hypothetical protein 0.34 — x x� 2862 3437892 3437957 65 Hypothetical protein — 0.2 — —� 2867 3445863 3445992 129 Coenzyme F390 synthetase/phenylacetyl-

CoA ligase0.2 — x —

� 2876 3454126 3453932 194 DNA polymerase IV 0.18 — — —� 2885 3468039 3468356 317 Metalloendopeptidases (putative) — 0.12 — —� 2887 3471568 3471499 69 Conserved protein 1.1 0.9 x x� 2897 3479706 3480004 298 Pirin — 0.14 x x� 2901 3485042 3484634 408 Transposase 0.26 0.9 x x� 2920 3510195 3510378 183 Ribosomal-protein-alanine

acetyltransferase— 0.2 — —

� 2929 3524542 3524596 54 Hypothetical protein 0.12 — — —� 2939 3541776 3541896 120 Serine O-acetyltransferase 0.22 0.2 x —� 2945 3549512 3549747 235 Mannosyltransferase — 0.18 x —



StrandORF

no. (1)


start (1)


(this work)5’-UTR


� 2948 3554303 3554336 33 Conserved protein — 0.14 — —� 2950 3556106 3556131 25 Conserved protein 0.42 0.38 x x� 2953 3562697 3562766 69 Transcriptional regulator — 0.18 x x� 2954 3563668 3563935 267 Transcriptional regulator — 0.2 x x� 2959 3572325 3572408 83 Hypothetical protein 0.12 0.38 x —� 2970 3588034 3587801 233 Conserved protein — 0.18 — —� 2999 3623024 3623369 345 Transposase 0.14 — x x� 3002 3627423 3627837 414 Hypothetical protein 0.16 0.36 x x� 3017 3646115 3646087 28 ABC transporter, permease protein 0.18 — — —� 3036 3672179 3672007 172 Hypothetical protein 0.26 — x —� 3045 3686319 3686612 293 Coenzyme F420 hydrogenase, alpha

subunit0.9 0.62 x —

� 3046 3687104 3686899 205 Conserved protein — 0.12 — —� 3048 3689682 3689848 166 Hypothetical protein — 0.14 — —� 3076 3730798 3730559 239 DNA topoisomerase I — 0.13 x x� 3079 3736283 3736087 196 Hypothetical protein 0.24 0.18 — —� 3086 3746722 3746587 135 Nicotinate phosphoribosyltransferase 0.27 0.18 — —� 3087 3749767 3750261 494 Hypothetical protein 0.36 0.32 x x� 3101 3771733 3771779 46 Two component system histidine kinase 0.22 0.32 x x� 3103 3773468 3773557 89 Hypothetical protein — 0.2 — —� 3104 3774022 3774034 12 Hypothetical protein 0.18 — x —� 3108 3777826 3777861 35 Hypothetical protein 0.48 0.26 x —� 3111 3783501 3783758 257 Hypothetical protein 0.14 — x x� 3112 3784019 3783992 27 Conserved protein 0.18 — x x� 3120 3793988 3794203 215 Hypothetical protein 0.14 — — —� 3124 3797989 3797894 95 Hypothetical protein — 0.12 x x� 3130 3803988 3804041 53 Hypothetical protein 0.12 0.2 x x� 3132 3806374 3806501 127 Hypothetical protein — 0.14 — —� 3169 3853910 3853965 55 Hypothetical protein — 0.14 x x� 3178 3863965 3863999 34 Hypothetical protein 1 0.38 x —� 3181 3867269 3867075 194 Ketoisovalerate oxidoreductase subunit — 0.12 — —� 3185 3873090 3873247 157 Ornithine decarboxylase — 0.14 x —� 3188 3876957 3876841 116 Glutamine synthetase 0.46 3.2 x x� 3195 3884185 3884293 108 Transcriptional regulator, MarR family — 0.14 x —� 3203 3895610 3895940 330 Hypothetical protein 0.12 — — —� 3212 3909480 3909885 405 Hypothetical protein — 0.14 — —� 3216 3915108 3915320 212 Conserved protein — 0.2 — —� 3231 3928421 3927974 447 Conserved protein 0.1 — — —� 3246 3946111 3946232 121 Transposase (N-terminal domain) 0.36 0.26 x x� 3257 3960178 3960512 334 Conserved protein 0.12 — x —� 3262 3964659 3964609 50 Branched-chain amino acid transport

protein0.1 — x —

� 3269 3973198 3973359 161 Serine O-acetyltransferase 0.17 — — —� 3271 3974828 3974964 136 Glutaredoxin 0.12 — x —� 3287 3998626 3998711 85 Hypothetical protein 0.14 — — —� 3288 3999805 3999782 23 Conserved protein 0.32 — x x� 3291 4007352 4007719 367 Excinuclease ABC, subunit A — 0.2 x —� 3300 4017939 4017643 296 Phosphoadenosine phosphosulfate

reductase0.22 0.12 x x

� 3301 4020895 4020625 270 Hypothetical protein 0.12 — x x� 3305 4025916 4025529 387 Putative DNA or RNA helicase of

superfamily II0.16 — — —

� 3306 4028835 4028708 127 Conserved protein — 0.12 x x� 3314 4036559 4036711 152 N-5’-phosphoribosyl)anthranilate

isomerase— 0.14 x x

� 3331 4059828 4059594 234 Conserved protein 0.16 — x x� 3340 4068085 4067921 164 Hypothetical protein — 0.12 — —� 3370 4095157 4095321 164 Hypothetical protein — 0.2 x —

The chromosomal location of the TSS and the distance to the annotated translational start codon (2) is indicated. The score indicates the relative clone numberper nucleotide within the enriched libraries.




Table S4. Leaderless mRNAs identified

StrandORF

no. (1)


start (1)


(this work) Gene function (1) �N score �N score TATA box BRE

� 19 23977 23977 Conserved protein 0.22 — x x� 161 208152 208152 Hypothetical protein 0.2 — x x� 251 334887 334893 Transposase 0.14 0.13 x x� 361 468816 468816 Transcriptional regulator, MarR family 0.19 — x x� 378 486448 486448 Sugar-phosphate nucleotidyltransferase 0.17 — x —� 383 489648 489648 Hypothetical protein 0.14 — x x� 443 564674 564675 Phosphoribosylglycinamide formyltransferase — 0.33 x x� 444 565795 565800 HTH DNA-binding protein 0.3 0.5 x x� 458 579716 579716 Cytidylyltransferase 0.11 0.13 x x� 459 580321 580321 Conserved protein 0.11 — — —� 648 779245 779246 Glycosyl transferase 0.14 0.13 x x� 732 881356 881348 Nitrogen regulatory protein P-II — 0.12 x —� 740 887595 887595 Transposase (N-terminal domain) 1.2 0.13 x x� 801 954914 954914 Adenylosuccinate synthetase 0.11 — x x� 831 981641 981641 Molybdopterin converting factor, small subunit — 0.18 x x� 872 1031252 1031260 Putative transcriptional regulator 0.9 — x x� 989 1166462 1166457 Conserved protein 0.21 — x x� 1082 1274097 1274097 GTP-binding protein 0.14 — x —� 1159 1379777 1379777 Hypothetical protein 0.32 0.14 — —� 1163 1383102 1383099 Nucleotidyltransferase 0.3 — x x� 1213 1436143 1436144 Aspartate carbamoyltransferase, catalytic subunit — 0.12 x x� 1276 1511119 1511118 Hypothetical protein 0.23 0.12 x x� 1298 1543848 1543854 Putative tRNA 2’phosphotransferase — 0.12 x x� 1332 1590040 1590040 Iron-dependent repressor 0.35 — x —� 1408 1691179 1691179 Archaeosine tRNA-ribosyltransferase — 0.18 — —� 1423 1705725 1705726 dCMP deaminase 0.24 — x x� 1520 1812498 1812499 Conserved protein 0.46 — x x� 1537 1835547 1835547 Conserved protein 0.1 0.18 x x� 1595 1899736 1899739 Conserved protein 0.4 0.12 x —� 1596 1900175 1900168 Conserved protein 0.7 — x x� 1605 1916206 1916203 Conserved protein 0.1 — — —� 1627 1940670 1940670 Fructose-bisphosphate aldolase 0.14 0.18 x x� 1712 2054237 2054237 Chorismate synthase 0.12 — x x� 1813 2162571 2162571 Conserved protein 0.21 0.23 — —� 1869 2219327 2219327 Conserved protein 0.13 — x x� 1873 2226770 2226770 Phosphohydrolase 0.14 — x —� 2018 2408623 2408621 Conserved protein 0.34 — x x� 2019 2410777 2410777 Phosphoribosyl-AMP cyclohydrolase — 0.12 x x� 2060 2455859 2455866 Histidinol-phosphate aminotransferase 1.3 — x —� 2114 2525927 2525918 Hypothetical protein 1.1 0.41 x x� 2117 2528662 2528659 Hypothetical protein 0.16 — x x� 2237 2668004 2668004 Transcriptional regulator, ArsR family — 0.14 x x� 2330 2788227 2788227 Hypothetical protein 0.1 0.12 x x� 2362 2819258 2819259 Shikimate kinase 0.12 — — —� 2367 2823290 2823289 Hexulose-6-phosphate isomerase — 0.18 — —� 2375 2832077 2832070 Conserved protein 1.6 1.1 x x� 2380 2838031 2838030 ATP-dependent DNA helicase — 0.24 x x� 2408 2870030 2870030 Conserved protein 0.12 — x —� 2525 3011382 3011376 Hypothetical protein 0.29 — x x� 2593 3088329 3088325 Hypothetical protein 0.1 — x x� 2686 3210641 3210645 Transposase — 0.14 — —� 2774 3327606 3327605 Conserved protein 0.21 0.1 x x� 2777 3329961 3329961 Acylphosphatase 0.1 — x —� 2835 3400631 3400632 Hypothetical protein 0.14 — x —� 2871 3449557 3449557 Hypothetical protein 0.2 — x —� 2877 3455326 3455325 Hypothetical protein 0.1 — x x� 2930 3526346 3526346 Hypothetical protein 0.12 — x x� 2956 3567192 3567196 Conserved protein 0.14 — x x� 3016 3646005 3646011 Cobalt transport ATP-binding protein CbiO — 0.12 x —� 3074 3729492 3729491 RNase P RNA component — 0.18 x x� 3155 3835149 3835156 Hypothetical protein 0.9 0.44 x x� 3184 3871702 3871709 Conserved protein 0.2 0.14 x —� 3199 3887532 3887530 Transporter 0.13 — — —� 3220 3918314 3918305 Transporter 0.13 — x —� 3264 3965865 3965859 F420 hydrogenase/dehydrogenase, beta subunit 0.1 0.12 x x� 3286 3996944 3996944 Hypothetical protein 0.32 — x x

The chromosomal location of the TSS and the distance to the annotated translational start codon (2) is indicated. The score indicates the relative clone numberper nucleotide within the enriched libraries.




Table S5. part I. sRNA candidates identified in IGRs of M. mazei Gö1

StrandAdjacentgenes (1)

Genomiccontext

orientationsRNA

candidate Function of adjacent genes (1) 5’ end 3’ end size �N score �N scoreSequence

conservation

� MM�0010/11 433 sRNA001 Hypothetical protein/Conservedprotein

11766 11792 26 — 0.25 —

� MM�0016/17 344 sRNA002 Translation initiation factor 1A(EIF-1A)/Ubiquinone/menaquinone biosynthesismethyltransferase

19212 18973 239 0.11 — MA, MB

� MM�0037/38 434 sRNA003 Argininosuccinate synthase/Carbamoyl-phosphate synthaselarge chain

45966 46003 37 — 0.12 —

� MM�0071/72 344 sRNA005 Conserved protein/Thermosomebeta-subunit

96443 96397 46 — 0.26 —

� MM�0077/78 334 sRNA006 Hypothetical protein/Xanthine-guaninephosphoribosyltransferase

103760 103823 63 — 0.20 —

� MM�0093/94 344 sRNA007 Cobyric acid synthase CbiP/Hypothetical protein

121850 121780 70 0.22 0.13 —

� MM�0117/18 434 sRNA008 Hypothetical protein/CTP synthase 145448 145494 46 — 0.12 —� MM�0117/18 444 sRNA009 Hypothetical protein/CTP synthase 146550 146466 84 1.40 0.42 —� MM�0124/25 333 sRNA010 Conserved protein/Universal stress

protein154820 154843 23 0.10 — —

� MM�0124/25 333 sRNA011 Conserved protein/Universal stressprotein

154954 154992 38 — 0.27 —


154985 154889 96 0.35 1.10 MA, MB

� MM�0128/29 433 sRNA013 ATP-dependent protease La/Conserved protein

161064 161082 18 — 0.20 —

� MM�0130/31 443 sRNA157 Conserved protein/Conservedprotein

162529 162341 188 — 0.14 MA

� MM�0136/37 433 sRNA014 Zn-dependent hydrolase/Conserved protein

171207 171234 27 — 0.40 —

� MM�0159/60 334 sRNA015 Hypothetical protein/Hypothetical protein

207470 207593 123 0.14 — —

� MM�0173/74 343 sRNA016 AdoCbi amidohydrolaseCbiZ/Methanol corrinoidprotein MtaC3

231666 231559 107 6.00 35.00 MA, MB

� MM�0183/84 344 sRNA017 DNA topoisomerase III/SSUribosomal protein S3AE

256806 256777 29 — 0.19 —

� MM�0198/99 434 sRNA018 ATP-dependent DNA helicase/Conserved protein

276808 276829 21 — 0.12 MA, MB

� MM�0206/07 334 sRNA019 Conserved protein/Hypotheticalprotein

282652 282714 62 — 0.20 MA, MB

� MM�0251/52 434 sRNA020 Transposase/Conserved protein 335007 335182 175 0.20 0.18 —� MM�0252/53 434 sRNA021 Conserved protein/Replication

factor c subunit336282 336365 83 0.50 0.70 —

� MM�0252/53 434 sRNA022 Conserved protein/Replicationfactor c subunit

336727 336912 185 0.40 1.60 MA

� MM�0259/60 433 sRNA023 Dihydroxy-acid dehydratase/Putative Sensory Transductionprotein Kinase

347388 347497 109 0.65 2.50 MB

� MM�0259/60 443 sRNA024 Dihydroxy-acid dehydratase/Putative Sensory Transductionprotein Kinase

347777 347751 26 — 0.13 —


352092 352068 24 — 0.13 —

� MM�0303/04 433 sRNA026 Hypothetical protein/AAA familyATPase

406893 406949 56 — 0.12 —

� MM�0303/04 443 sRNA027 Hypothetical protein/AAA familyATPase

406924 406708 216 0.14 — MA, MB

� MM�0392/93 334 sRNA028 Hypothetical protein similar toC-terminal domain of HdrB/Conserved protein

505478 505542 64 — 0.18 MA




Genomiccontext

orientationsRNA


conservation


513394 513542 148 — 0.25 MA

� MM�0402/03 433 sRNA030 Conserved protein/Hypotheticalprotein similar to C-terminaldomain of HdrB

515427 515497 70 0.70 5.00 MA, MB

� MM�0422/23 344 sRNA031 Transposase/Conserved protein 537016 536982 34 0.11 — MA, MB� MM�0446/47 433 sRNA032 NAD � synthetase/Cell division

control protein (AAA familyATPase)

568422 568487 65 — 0.90 MA


573826 573719 107 — 0.13 MB

� MM�0530/31 434 sRNA034 Amino acid permease/Conservedprotein

659997 660032 35 0.26 — —


679306 679287 19 — 0.20 MA, MB

� MM�0574/75 334 sRNA036 Arsenate reductase/Putativephosphate regulatory protein

701671 701696 25 — 0.20 MA

� MM�0578/79 444 sRNA037 Phosphate-binding protein/Transposase

705833 705793 40 — 0.27 —


708500 708555 55 — 0.13 —

� MM�0582/83 343 sRNA039 Glycosyltransferase/Conservedprotein

711809 711694 115 0.39 — MA, MB


747100 747126 26 0.14 — MA, MB

� MM�0666/67 344 sRNA041 Putative nickel-responsiveregulator NikR/Nitroreductasefamily protein

800086 799881 205 20.00 0.24 MA, MB

� MM�0671/72 434 sRNA042 2-Isopropylmalate synthase/Hypothetical protein

806578 806603 25 — 0.13 MB

� MM�0671/72 434 sRNA043 2-Isopropylmalate synthase/Hypothetical protein

806578 806603 25 0.35 0.38 MB

� MM�0696/97 433 sRNA044 Beta-phosphoglucomutase/Celldivision protein

835924 835958 34 — 0.20 —

� MM�0699/700

334 sRNA045 Conserved protein/Vacuolar-typeH�-pyrophosphatase

840527 840820 293 8.00 3.50 MA

� MM�0700/01 443 sRNA046 Vacuolar-typeH�-pyrophosphatase/Vacuolar-typeH�-pyrophosphatase

843370 843307 63 — 0.13 —

� MM�0701/02 343 sRNA047 Vacuolar-typeH�-pyrophosphatase/Hypothetical permease

846629 846462 167 3.70 1.70 MA, MB

� MM�0729/30 434 sRNA048 Conserved protein/SAM-dependentmethyltransferases

880183 880258 75 — 0.12 —

� MM�0760/61 433 sRNA049 Ferredoxin/Thiamin-monophosphate kinase

908968 908989 21 — 0.20 MA

� MM�0777/78 434 sRNA050 Hydrogenase maturation protein/A1AO H � ATPASE, SUBUNIT D

930869 930925 56 — 0.17 MA, MB

� MM�0816/17 344 sRNA051 Transposase/Pyrroline-5-carboxylate reductase

967401 967341 60 0.14 0.38 —


978485 978538 53 — 0.13 —

� MM�0854/55 443 sRNA053 Cell division cycle protein 48homolog/Phosphoribosylamidoimidazole-succinocarboxamide synthase

1009500 1009477 23 — 0.13 —

� MM�0858/59 433 sRNA054 Protein translation initiationfactor 1 (IF-1)/Conservedprotein

1012758 1012814 56 — 0.13 MA, MB

� MM�0867/68 334 sRNA055 Methionyl-tRNA synthetase/Adenylate cyclase

1026994 1027106 112 — 0.32 —




Genomiccontext

orientationsRNA


conservation

� MM�0880/81 334 sRNA056 Conserved protein/Transposase 1039768 1039820 52 — 0.12 MA� MM�0907/08 434 sRNA057 Hypothetical protein/Conserved

protein1073867 1074062 195 0.23 1.40 MA

� MM�0921/22 333 sRNA058 Aldehyde ferredoxinoxidoreductase/Proteiniranslation initiation factor 5A(IF-5A)

1088900 1088932 32 — 0.55 —

� MM�0923/24 334 sRNA059 Agmatinase/Conserved protein 1090823 1090937 114 — 0.14 —� MM�0940/41 334 sRNA060 Putative flavodoxin

/Adenylosuccinate lyase1114177 1114265 88 0.90 1.70 MA

� MM�0940/41 434 sRNA061 Putative flavodoxin/Adenylosuccinate lyase

1114828 1114977 149 2.30 1.90 MA

� MM�0954/55 334 sRNA062 Hypothetical protein/ABCtransporter, permease protein

1134433 1134515 82 — 0.12 —

� MM�0964/65 333 sRNA063 Glutamine synthetase/Hypothetical protein

1143569 1143595 26 — 0.18 —

� MM�1000/1 333 sRNA064 Precorrin-6Y C5,15-methyltransferase�decarboxylating�

/2-Isopropylmalate synthase

1175279 1175306 27 — 0.25 —

� MM�1032/33 444 sRNA065 Conserved protein/Ferrous irontransport protein B

1208072 1208045 27 0.35 0.53 —

� MM�1072/73 333 sRNA066 Conserved protein/Methanolcorrinoid protein MtaC2

1261239 1261343 104 — 0.58 —


1261248 1261107 141 0.10 — MA


1261471 1261571 100 0.16 0.12 —

� MM�1093/94 343 sRNA069 Hypothetical sensory transductionhistidine kinase/Putativetranscriptional regulator

1287565 1287443 122 0.11 — —

� MM�1117/18 433 sRNA070 Polysaccharide deacetylase/Conserved protein

1312862 1312926 64 — 0.20 MA

� MM�1131/32 433 sRNA071 Hypothetical protein/UDP-glucose 6-dehydrogenase

1334884 1334922 38 — 0.24 —


1409359 1409382 23 — 0.13 —

� MM�1253/54 444 sRNA073 Cation transporter/Putative heatshock protein

1488803 1488632 171 0.51 0.42 —

� MM�1298/99 443 sRNA074 Putative tRNA2’phosphotransferase/Replication factor-A protein

1544467 1544425 42 — 0.24 —


1594821 1595010 189 1.80 1.10 —

� MM�1348/49 343 sRNA076 Arginyl-tRNA synthetase/Conserved protein

1617533 1617505 28 — 0.20 —

� MM�1399/40 443 sRNA077 MutT-like protein/Hypotheticalprotein

1683118 1683085 33 — 0.14 —

� MM�1440/41 343 sRNA078 Conserved protein/Inorganicpyrophosphatase

1723544 1723464 80 — 0.12 MA, MB

� MM�1441/42 334 sRNA079 Inorganic pyrophosphatase/Hypothetical protein

1724290 1724347 57 — 0.12 —

� MM�1485/86 343 sRNA080 Conserved protein/Alanyl-tRNAsynthetase

1769596 1769411 185 0.24 — MA


1780407 1780472 65 — 0.11 —

� MM�1502/03 433 sRNA158 S-adenosylmethionine synthetase/ATP phosphoribosyltransferase

1792230 1792303 73 0.20 1.00 MA

� MM�1527/28 434 sRNA082 Citrate (si) synthase/Aconitatehydratase

1822377 1822476 99 — 0.12 —

� MM�1589/90 443 sRNA083 Surface layer protein (putative)/Conserved protein

1894706 1894670 36 0.20 0.44 —




Genomiccontext

orientationsRNA


conservation

� MM�1604/05 443 sRNA084 Tungsten formylmethanofurandehydrogenase subunit E/Conserved protein

1915379 1915284 95 0.20 — MA, MB

� MM�1604/05 443 sRNA085 Tungsten formylmethanofurandehydrogenase subunit E/Conserved protein

1915909 1915804 105 0.50 — MA, MB

� MM�1615/16 343 sRNA086 Oxidoreductase, aldo/keto family/Phosphoribosylaminoimidazolecarboxylase

1927673 1927521 152 0.12 0.10 MA, MB

� MM�1716/17 443 sRNA087 Transcriptional regulator, ArsRfamily/Conserved protein

2060959 2060895 64 3.20 8.00 MA, MB


2061136 2061100 36 — 0.14 —

� MM�1721/22 443 sRNA089 Transcriptional regulator, ArsRfamily/Hypothetical protein

2066165 2066098 67 1.10 3.80 MA, MB

� MM�1732/33 443 sRNA090 Transcriptional regulator, ArsRfamily/Metalloproteinase

2075070 2074994 76 0.86 2.60 MA, MB


2130503 2130538 35 — 0.17 —

� MM�1820/21 333 sRNA092 tRNA nucleotidyltransferase/Replication factor c subunit

2172639 2172683 44 — 0.17 —

� MM�1838/39 443 sRNA093 Ferredoxin/Conserved protein 2190331 2190268 63 0.14 1.20 —� MM�1870/71 334 sRNA094 Conserved protein/Vanillate

decarboxylase protein2223513 2223580 67 0.28 0.86

� MM�1967/68 343 sRNA095 Hypothetical protein/Cupin-typephosphoglucose isomerases

2337964 2337838 126 0.12 — —

� MM�1973/74 444 sRNA096 Conserved protein/Histoneacetyltransferase (ELP3 faminly)

2343191 2343154 37 — 0.32 —


2343492 2343360 132 — 0.13 —


2343494 2343417 77 — 0.20 —


2419520 2419489 31 — 0.52 —

� MM�2245/46 434 sRNA100 Conserved protein/Transcriptional regulator, ArsRfamily

2673782 2673887 105 — 0.29 —

� MM�2305/06 434 sRNA101 Sodium/proline symporter/L-asparaginase

2760525 2760711 186 0.13 — MA, MB

� MM�2335/36 343 sRNA102 Conserved protein/Translationinitiation factor 1A (EIF-1A)

2793547 2793474 73 0.14 0.56 —

� MM�2368/69 343 sRNA159 Aspartate aminotransferase/Cytochrome c-type biogenesisprotein

2825468 2825442 26 — 0.46 —

� MM�2405/06 443 sRNA104 Cation transporter/Conservedprotein

2867335 2867271 64 — 0.14 MA, MB


2868198 2868264 66 — 0.12 —


2873129 2873057 72 0.12 0.60 MA, MB


2915319 2915256 63 0.14 0.32 MA

� MM�2491/92 433 sRNA160 F420H2 dehydrogenase, subunitA/Putative Ferredoxin

2969755 2969933 178 — 0.35 MA, MB

� MM�2498/99 343 sRNA107 Conserved protein/Geranylgeranyl reductase

2977003 2976951 52 — 0.18 —

� MM�2498/99 333 sRNA108 Conserved protein/Geranylgeranyl reductase

2977245 2977304 59 — 0.18 —

� MM�2505/06 434 sRNA109 Chaperone protein/GrpE protein 2988840 2988997 157 0.13 — —� MM�2514/15 333 sRNA110 Archaeal protein Translation

Elongation Factor 1, subunitbeta/Hypothetical sensorytransduction histidine kinase

2997835 2997910 75 0.13 0.18 MA




Genomiccontext

orientationsRNA


conservation


3020206 3020109 97 0.22 — —

� MM�2565/66 343 sRNA112 Pyruvate formate-lyase activatingenzyme/CODH nickel-insertionaccessory protein CooC

3055009 3054933 76 — 0.20 —

� MM�2585/86 443 sRNA113 Sec-independent proteintranslocase, protein/Sec-independent proteintranslocase, protein

3074333 3074296 37 — 0.24 —

� MM�2590/91 343 sRNA114 Transposase/Hypothetical protein 3080296 3080172 124 0.14 0.12 MA� MM�2619/20 343 sRNA115 Hypothetical protein/

Proteasome, subunit-alpha3122483 3122456 27 0.12 0.18 MA, MB


3136199 3136235 36 — 0.35 —

� MM�2636/37 344 sRNA117 Coenzyme F390 synthetase/phenylacetyl-CoAligase/Hypothetical protein

3144836 3144761 75 0.20 — —

� MM�2655/56 334 sRNA118 Hypothetical protein/Peptidyl-prolyl cis-transisomerase

3173527 3173664 137 1.40 — —


3193405 3193305 100 — 0.20 —


3261756 3261650 106 0.20 0.32 MB


3261968 3261908 60 0.14 0.14 MA, MB

� MM�2748/49 343 sRNA122 Hypothetical sensory transductionhistidine kinase/Aminoacyl-histidinedipeptidase

3293888 3293839 49 — 0.14 —


3300072 3300097 25 0.70 0.90 —

� MM�2777/78 334 sRNA161 Acylphosphatase/Cobalt-zinc-cadmium resistanceprotein

3330273 3330387 114 0.24 — —

� MM�2797/98 343 sRNA124 Pirin/Conserved protein 3356686 3356386 300 12.00 4.00 MA, MB� MM�2805/06 443 sRNA125 Asparagine synthetase

�glutamine-hydrolyzing�


3368790 3368769 21 0.12 — MA

� MM�2807/08 334 sRNA126 Phosphoribosylformylglycina-midine synthase/Conserved pro-tein

3370460 3370697 237 4.00 2.90 MA, MB

� MM�2835/36 433 sRNA127 Hypothetical protein/Enolase 3400842 3401003 161 0.16 — MA� MM�2854/55 343 sRNA128 Hypothetical protein/ABC

transporter, permease protein3428150 3428014 136 — 0.14 MA, MB

� MM�2885/86 434 sRNA129 Metalloendopeptidases(putative)/Hypothetical sensorytransduction histidine kinase

3468324 3468574 250 1.20 2.00 MA, MB

� MM�2885/86 444 sRNA130 Metalloendopeptidases(putative)/Hypothetical sensorytransduction histidine kinase

3468422 3468387 35 — 0.14 MA, MB

� MM�2927/28 444 sRNA131 Heteropolysaccharide repeat unitexport protein/Hypotheticalprotein

3522028 3521977 51 — 0.26 MA


3556473 3556167 306 2.00 0.20 MA

� MM�2956/57 433 sRNA133 Conserved protein/Transposase 3567455 3567683 228 0.16 — —� MM�2957/58 334 sRNA134 Transposase/Conserved protein 3569603 3569769 166 0.78 1.60 —� MM�3111/12 443 sRNA135 Hypothetical protein/Conserved

protein3783938 3783838 100 0.12 0.14 —

� MM�3113/14 433 sRNA136 Oligoendopeptidase F/Conservedprotein

3786460 3786491 31 0.16 — —




Genomiccontext

orientationsRNA


conservation

� MM�3137/38 444 sRNA137 TRANSPORTER, LysE family/Cob(I)alaminadenosyltransferase

3812709 3812625 84 0.18 0.44 —

� MM�3139/40 443 sRNA138 Large-conductancemechanosensitive channel/Flavodoxin

3814424 3814369 55 — 0.14 —

� MM�3156/57 334 sRNA139 OXIDOREDUCTASE/Putative6-aminohexanoate-dimerhydrolase

3836815 3836864 49 — 0.30 —

� MM�3157/58 443 sRNA140 Putative 6-aminohexanoate-dimer hydrolase/Hypotheticalprotein

3839149 3839087 62 — 0.14 —


3847600 3847576 24 — 0.16 —


3859809 3859875 66 — 0.12 —

� MM�3183/84 334 sRNA143 Ketoisovalerate oxidoreductasesubunit/Conserved protein

3870097 3870168 71 0.13 — —


3870292 3870349 57 — 0.71 — MA


3870917 3870821 96 1.80 1.90 —MA, MB


3871270 3871088 182 5.20 5.00 MA, MB

� MM�3206/07 433 sRNA147 Response regulator/Protease(putative)

3901326 3901461 135 — 0.12 —


3915944 3915881 63 — 0.14 —


3957690 3957668 22 — 0.20 —


3957990 3957764 226 0.42 — MA

� MM�3265/66 344 sRNA151 Transposase/Hypothetical protein 3969321 3969187 134 0.70 — —� MM�3280/81 434 sRNA152 Conserved protein/

SAM-dependentmethyltransferases

3989606 3989626 20 — 0.12 —

� MM�3324/25 433 sRNA153 Oligopeptide transporter,ATP-binding protein/Permease,Na�/H�-dicarboxylatesymporter

4050456 4050507 51 0.34 — —


4065452 4065321 131 — 1.00 MA, MB


4067977 4067902 75 — 0.20 —


4069363 4069207 156 2.20 1.20 MB

Besides the genomic context of the sRNA candidates, the respective score under N-limitation and N-sufficiency indicating the relative clone number pernucleotide within the enriched libraries is shown as well as conservation in other Methanosarcinales. MB, M. barkeri; MA, M. acetivorans.




Table S5. part II. sRNA candidates in M. mazei Gö1 complementary and overlapping with 5’ or 3’ regions of mRNAs (asRNAs)

StrandAdjacentgens (1)

Genomiccontext

orientationasRNA

candidate Function of adjacent genes (1) 5’ end 3’ end Size �N score �N scoreSequence

conservation

� MM�3371/0001 443 asRNA001 Annotation/ Prognose/DipeptideABC transporter, bindingprotein

333 293 40 0.10 0.32 —

� MM�0052/53 434 asRNA047 Transposase/Hypothetical protein 70614 70782 168 0.40 1.20 MA, MB� MM�0089/90 434 asRNA002 Hypothetical protein/Conserved

protein115503 115737 234 0.15 — MA

� MM�0152/53 433 asRNA003 DNA integration/recombination/invertion protein/Conservedprotein

193140 193180 40 0.11 0.55 MA, MB

� MM�0257/58 343 asRNA004 Hypothetical protein/Transposase 343417 343312 105 0.11 0.13 MA, MB� MM�0355/56 433 asRNA049 Transposase/Hypothetical protein 462532 462659 127 10 15.00 MA, MB� MM�0398/99 433 asRNA005 Conserved protein/Hypothetical

protein similar to C-terminaldomain of HdrB

511908 511981 73 — 0.28 MA, MB

� MM�0616/17 443 asRNA006 Conserved protein/Conservedprotein

748748 748725 23 — 0.13 MA, MB

� MM�0700/01 433 asRNA007 Vacuolar-typeH�-pyrophosphatase/Vacuolar-typeH�-pyrophosphatase

843060 843085 25 — 0.40 MA

� MM�0710/11 443 asRNA008 Hypothetical protein/Transposase 856744 856688 56 0.60 8.60 —� MM�0787/88 434 asRNA045 Transposase/Metallo cofactor

biosynthesis protein (moaA/nifB/pqqE family)

940551 940749 198 0.23 0.35 MA, MB

� MM�0881/82 433 asRNA048 Transposase/Hypothetical protein 1041288 1041511 223 5.70 19.00 MA, MB� MM�0971/72 433 asRNA009 Hypothetical protein/Conserved

protein1150834 1150903 69 0.26 0.46 MA, MB

� MM�1042/43 343 asRNA010 Transcriptional regulator/Transposase

1219157 1219116 41 — 0.13 —

� MM�1072/73 343 asRNA011 Conserved protein/Methanolcorrinoid protein MtaC2

1260553 1260358 195 0.65 0.10 —

� MM�1088/89 343 asRNA012 ABC transporter, ATP-bindingprotein/Putative DNAintegration/recombination/invertion protein

1281930 1281783 147 0.90 1.10 MA, MB

� MM�1105/06 334 asRNA013 Metallo cofactor biosynthesisprotein (moaA/ nifB/pqqEfamily)/Putative phosphoserinephosphatase

1299787 1299840 53 — 0.10 —

� MM�1198/99 433 asRNA014 Transposase/Conserved protein 1425029 1425102 73 12.00 33.00 MA, MB� MM�1432/33 344 asRNA015 Hypothetical protein/

Hypothetical protein1714942 1714893 49 — 0.12 —

� MM�1432/33 334 asRNA016 Hypothetical protein/Hypothetical protein

1714973 1715013 40 0.13 0.35 —

� MM�1501/02 434 asRNA017 Hypothetical protein/S-adenosylmethioninesynthetase

1790663 1790931 268 0.10 — MA

� MM�1520/21 443 asRNA018 Conserved protein/Phosphoglucomutase/phosphomannomutase

1812687 1812666 21 — 0.18 —

� MM�1527/28 434 asRNA019 Citrate (si) synthase/Aconitatehydratase

1822201 1822231 30 0.38 0.90 MA

� MM�1768/69 344 asRNA043 Transposase/Pyruvate, phosphatedikinase

2110899 2110771 128 0.56 0.20 MA, MB

� MM�1781/82 343 asRNA020 Hypthetical sensory transductionhistidine kinase/Sodium/glutamate symportcarrier protein

2128249 2128218 31 — 0.26 —


2201965 2201934 31 — 0.14 MA



StrandAdjacentgens (1)

Genomiccontext

orientationasRNA


conservation

� MM�1915/16 343 asRNA022 Hypothetical sensorytransduction histidinekinase/Lysyl-tRNA synthetase,class II

2276356 2276237 119 0.14 — —


2419355 2419115 240 2.80 0.12 MB

� MM�2033/34 443 asRNA024 Stomatin-like protein/Conservedprotein

2430653 2430561 92 — 0.12 —

� MM�2038/39 433 asRNA025 Conserved protein/SSU ribosomalprotein S8E

2436228 2436261 33 — 0.12 —

� MM�2337/38 343 asRNA026 Conserved protein/Conservedprotein in Methanosarcinaspec.

2795267 2795230 37 — 0.30 —

� MM�2375/76 344 asRNA028 Conserved protein/Conservedprotein

2833331 2833091 240 7.40 — —

� MM�2390/91 434 asRNA044 Transposase/Hypothetical protein 2851716 2851779 63 0.11 0.35 MB� MM�2391/92 344 asRNA029 Hypothetical protein/

Long-chain-fatty-acid-CoAligase

2853018 2852900 118 0.28 0.20 MA, MB

� MM�2448/49 343 asRNA031 Transposase/Conserved protein 2921863 2921799 64 0.18 0.20 MA, MB� MM�2460/61 433 asRNA032 Dipeptide/oligopeptide-binding

protein/Conserved protein2936104 2936130 26 0.16 — —

� MM�2470/71 434 asRNA033 Surface layer protein (putative)/Hypothetical protein

2949766 2949904 138 0.10 — —

� MM�2572/73 334 asRNA034 Methyltransferase/Irondependent transcriptionalrepressor

3064136 3064185 49 0.16 0.35 —

� MM�2653/54 434 asRNA035 N5,N10-methenyltetrahy-dromethanopterin cyclohydro-lase/Hypothetical protein

3169314 3169335 21 — 0.12 —

� MM�2681/82 433 asRNA050 Hypothetical protein/Transposase 3205729 3205750 21 0.16 0.18 —� MM�2686/87 434 asRNA036 Transposase/Hypothetical protein 3210618 3210670 52 0.27 1.10 —� MM�2699/2700 343 asRNA046 Transposase/Hypothetical protein 3224219 3224005 214 0.2 0.8 MA� MM�2749/50 334 asRNA037 Aminoacyl-histidine dipeptidase/


� MM�2862/63 434 asRNA038 Hypothetical protein/Conservedprotein

3438100 3438246 146 1.10 1.30 MA

� MM�2957/58 344 asRNA039 Transposase/Conserved protein 3569565 3569329 236 0.14 — MA, MB� MM�2959/60 433 asRNA040 Hypothetical protein/


� MM�3167/68 334 asRNA041 Transposase/Conserved protein 3851969 3852065 96 0.70 2.90 MA� MM�3216/17 434 asRNA042 Conserved protein/Conserved

protein3915754 3916009 255 0.13 — —




Table S6. sRNA candidates located in IGRs in M. mazei Gö1 containing potential small ORFs (spRNAs)


Genomiccontext

orientationspRNA


conservation

� MM�0090/91 444 spRNA01 Conserved protein/ABCtransporter, permease protein

116807 116699 108 1.8 0.52 MA, MB

� MM�0178/79 343 spRNA03 Conserved protein/Conservedprotein

249071 248814 257 1.7 0.18 —

� MM�0188/89 344 spRNA04 Putative nucleotidyltransferase/Conserved protein

260955 260723 232 0.17 — —

� MM�0268/69 443 spRNA05 Conserved protein/Hypotheticalprotein

359868 359652 216 2.3 0.9 MA, MB

� MM�0617/18 343 spRNA06 Conserved protein/Undecaprenylpyrophosphate synthetase

749532 749302 230 0.17 0.13 —

� MM�0822/23 443 spRNA07 Hypothetical protein/Conservedprotein

973952 973762 190 1 0.7 MA, MB

� MM�0892/93 433 spRNA08 Hypothetical protein/Cobalaminbiosynthesis protein CbiM

1053914 1054068 154 0.16 — MA

� MM�0940/41 344 spRNA09 Putative flavodoxin/Adenylosuccinate lyase

1114307 1114086 221 1.3 1.1 MA

� MM�0940/41 444 spRNA10 Putative flavodoxin/Adenylosuccinate lyase

1114969 1114698 271 1.4 0.9 MA

� MM�1000/01 433 spRNA11 Precorrin-6Y C5,15-methyltransferase�decarboxylating�/2-Isopropylmalate synthase

1174850 1175143 293 0.35 0.12 MA

� MM�1052/53 344 spRNA12 Conserved protein/PutativeSensory protein

1231028 1230920 108 0.19 0.13 MA

� MM�1052/53 344 spRNA13 Conserved protein/PutativeSensory protein

1231482 1231295 187 1.1 0.3 —

� MM�1055/56 344 spRNA14 Trimethylamine corrionidprotein/PutativeATP-dependent Na� effluxpump

1238211 1237971 240 0.1 0.11 MA, MB

� MM�1432/33 433 spRNA15 Hypothetical protein/Hypotheticalprotein

1714676 1714902 226 9.5 2.6 MA, MB

� MM�1521/22 334 spRNA17 Phosphoglucomutase/phosphomannomutase/PutativeFeS oxidoreductase

1814494 1814730 236 1.3 — —

� MM�1539/40 434 spRNA18 Hypothetical protein/TetrahydromethanopterinS-methyltransferase, subunit H

1839412 1839674 262 0.21 0.18 —

� MM�1622/23 434 spRNA19 Conserved protein/Transposase(N-terminal domain)

1934592 1934684 92 0.16 — —

� MM�1710/11 343 spRNA20 3,4 Dihydroxy-2-butanone4-phosphate synthase/Cobalt-zinc-cadmium resistanceprotein

2053262 2053236 26 — 0.14 —

� MM�1764/65 333 spRNA21 Isopentenyl-diphosphatedelta-isomerase /Hypotheticalprotein

2104951 2105142 191 0.1 0.18 MA

� MM�1838/39 434 spRNA23 Ferredoxin/Conserved protein 2190267 2190330 63 0.11 — —� MM�1870/71 344 spRNA24 Conserved protein/Vanillate

decarboxylase protein2223610 2223356 254 0.9 0.45 MB

� MM�1938/39 333 spRNA25 Hypothetical protein/Glutamine-binding protein

2306915 2306966 51 0.11 0.13 —

� MM�2083/84 334 spRNA26 Orotidine 5’-phosphatedecarboxylase/COdehydrogenase/acetyl-CoAsynthase, gamma subunit

2483727 2483786 59 — 0.24 MA, MB

� MM�2089/90 443 spRNA27 CO dehydrogenase/acetyl-CoAsynthase, alpha subunit/HTHDNA-binding protein

2494143 2494011 132 0.18 — MA, MB

� MM�2098/99 444 spRNA28 Conserved protein/Hypotheticalprotein

2506609 2506556 53 0.16 0.38 —




Genomiccontext

orientationspRNA


conservation

� MM�2274/75 434 spRNA29 DNA-directed RNA polymerase,subunit H /Hypothetical sensorytransduction histidine kinase

2703234 2703511 277 0.74 0.23 MA, MB

� MM�2290/91 334 spRNA30 Cell surface protein/Zincmetalloprotease

2731075 2731191 116 0.18 — —

� MM�2295/95 433 spRNA31 Type I restriction-modificationsystem methylationsubunit/Surface layer protein(putative)

2739252 2739377 125 — 0.28 MA

� MM�2350/51 434 spRNA32 O-linked N-acetyglucosaminetransferase /Transcriptionalregulator

2809844 2809953 109 0.13 — MA, MB


2832992 2833159 167 0.64 — MA

� MM�2536/37 333 spRNA34 LSU ribosomal proteinL21E/Hypothetical protein

3023963 3024199 236 0.16 0.46 MA, MB

� MM�2557/58 343 spRNA35 Catalase/Hypothetical protein 3043639 3043407 232 0.42 0.12 MA, MB� MM�2565/66 333 spRNA36 CODH nickel-insertion accessory

protein CooC/ABC transporter,periplasmic binding protein

3056186 3056396 210 — 0.42 MA, MB

� MM�2610/11 444 spRNA37 Type I restrictionenzyme/Hypothetical protein

3107665 3107543 122 0.72 — MA, MB


3586527 3586748 221 — 0.12 MA

� MM�3094/95 333 spRNA40 Hypothetical protein/ABCtransporter, ATP-bindingprotein

3759938 3760177 239 0.16 — MA, MB

� MM�3137/38 344 spRNA41 Transporter, LysEfamily/Cob(I)alaminadenosyltransferase

3812475 3812382 93 0.14 — MA, MB


3913870 3914027 157 0.13 — —

� MM�3265/66 434 spRNA43 Transposase/Hypothetical protein 3968682 3968838 156 0.13 — —� MM�3352/53 434 spRNA44 Hypothetical protein/Conserved

protein4080081 4080344 263 0.7 1 MB

Besides the genomic context the respective score under N-limitation and N-sufficiency indicating the relative clone number per nucleotide within the enrichedlibraries is shown as well as conservation in other Methanosarcinales. MB, M. barkeri; MA, M. acetivorans.




Table S7. Random nothern blot analysis

Strand IGR

Genomiccontext

orientation(1) Transcript

Function of adjacentgenes (1) 5’ end 3’ end Size �N score �N score

Northernblot

regulation

Transcriptlength

determined

� MM�0010/11 433 sRNA001 Hypothetical protein/Conserved protein

11766 11792 26 — 0.25 0.81 880, 90 bp

� MM�0015/16 434 MM3372 Putativemethyltransferase/Translation initiationfactor 1A (EIF-1A)

17483 17859 376 15.00 5.00 1.39 600 bp

� MM�0015/16 434 MM3373 Putativemethyltransferase/Translation initiationfactor 1A (EIF-1A)

18203 18365 162 0.35 — 1.28 700 bp

� MM�0016/17 344 sRNA002 Translation initiationfactor 1A (EIF-1A)/Ubiquinone/menaquinonebiosynthesismethyltransferase

19212 18973 239 0.11 — — n.d.

� MM�0037/38 434 sRNA003 Argininosuccinatesynthase/Carbamoyl-phosphate synthaselarge chain

45966 46003 37 — 0.12 — n.d.

� MM�0039/40 433 MM3374 Carbamoyl-phosphatesynthase small chain/Glycine betainetransporter,ATP-binding protein(OtaA)

50714 50806 92 0.14 0.25 1.13 120 bp

� MM�0046/47 344 MM3375 Hypotheticalprotein/Acetylornithineaminotransferase

61498 61380 118 0.19 0.19 1.13 160, 120 bp

� MM�0052/53 434 asRNA047 Transposase/Hypothetical protein

70614 70782 168 0.40 1.20 0.95 160 bp

� MM�0071/72 344 sRNA005 Conservedprotein/Thermosomebeta-subunit

96443 96397 46 — 0.26 0.98 120 bp

� MM�0077/78 334 sRNA006 Hypothetical protein/Xanthine-guaninephosphoribosyltrans-ferase

103760 103823 63 — 0.20 — n.d.

� MM�0089/90 434 asRNA002 Hypothetical protein/Conserved protein

115503 115737 234 0.15 — — n.d.

� MM�0090/91 444 spRNA01 Conserved protein/ABCtransporter,permease protein

116807 116699 108 1.8 0.52 0.38 90, 150 bp

� MM�0093/94 344 sRNA007 Cobyric acid synthaseCbiP/Hypotheticalprotein

121850 121780 70 0.22 0.13 1.00 120 bp

� MM�0117/18 434 sRNA008 Hypothetical protein/CTP synthase

145448 145494 46 — 0.12 — n.d.

� MM�0117/18 444 sRNA009 Hypothetical protein/CTP synthase

146550 146466 84 1.40 0.42 0.87 70 bp

� MM�0117/18 444 MM3376 Hypothetical protein/CTP synthase

146454 146150 304 1.60 0.70 0.75 320 bp


154820 154843 23 0.10 — — n.d.


154954 154992 38 — 0.27 — n.d.



Strand IGR

Genomiccontext



Northernblot

regulation

Transcriptlength

determined


154985 154889 96 0.35 1.10 1.36 90, 110 bp

� MM�0128/29 433 sRNA013 ATP-dependentproteaseLa/Conservedprotein

161064 161082 18 — 0.20 — n.d.

� MM�0130/31 443 sRNA157 Conserved protein/Conserved protein

162529 162341 188 — 0.14 — n.d.

� MM�0131/32 343 MM3377 Conserved protein/Conserved protein

164001 163800 201 0.14 — — n.d.

� MM�0136/37 433 sRNA014 Zn-dependenthydrolase/Conserved protein

171207 171234 27 — 0.40 — n.d.

� MM�0151/52 434 MM3378 Conservedprotein/DNAintegration/recombination/invertion protein

191211 191336 125 0.23 — 0.96 120 bp

� MM�0152/53 433 asRNA003 DNAintegration/recombination/invertionprotein/Conservedprotein

193140 193180 40 0.11 0.55 1.04 90 bp


207470 207593 123 0.14 — — n.d.

� MM�0173/74 343 sRNA016 AdoCbiamidohydrolaseCbiZ/Methanolcorrinoid proteinMtaC3

231666 231559 107 6.00 35.00 1.22 130, 150 bp

� MM�0178/79 343 spRNA03 Conservedprotein/Conservedprotein

249071 248814 257 1.7 0.18 0.62 80 bp

� MM�0183/84 344 sRNA017 DNA topoisomeraseIII/SSU ribosomalprotein S3AE

256806 256777 29 — 0.19 — n.d.

� MM�0188/89 344 spRNA04 Putativenucleotidyltransferase/Conservedprotein

260955 260723 232 0.17 — — n.d.

� MM�0198/99 434 sRNA018 ATP-dependent DNAhelicase/Conservedprotein

276808 276829 21 — 0.12 — n.d.

� MM�0206/07 334 sRNA019 Conserved protein/Hypothetical protein

282652 282714 62 — 0.20 0.95 70, 120 bp

� MM�0251/52 434 sRNA020 Transposase/Conservedprotein

335007 335182 175 0.20 0.18 1.11 80 bp

� MM�0252/53 434 sRNA021 Conserved protein/Replication factor csubunit

336282 336365 83 0.50 0.70 — n.d.

� MM�0252/53 434 sRNA022 Conserved protein/Replication factor csubunit

336727 336912 185 0.40 1.60 1.02 130, 150 bp

� MM�0257/58 343 asRNA004 Hypothetical protein/Transposase

343417 343312 105 0.11 0.13 — n.d.

� MM�0259/60 433 sRNA023 Dihydroxy-aciddehydratase/Putative SensoryTransduction proteinKinase

347388 347497 109 0.65 2.50 0.89 90 bp



Strand IGR

Genomiccontext



Northernblot

regulation

Transcriptlength

determined

� MM�0259/60 443 sRNA024 Dihydroxy-aciddehydratase/Putative SensoryTransduction proteinKinase

347777 347751 26 — 0.13 — n.d.

� MM�0262/63 444 sRNA025 Conserved protein/Conserved protein

352092 352068 24 — 0.13 — n.d.

� MM�0268/69 443 spRNA05 Conserved protein/Hypothetical protein

359868 359652 216 2.3 0.9 1.21 70, 680 bp

� MM�0303/04 433 sRNA026 Hypotheticalprotein/AAA familyATPase

406893 406949 56 — 0.12 — n.d.

� MM�0303/04 443 sRNA027 Hypotheticalprotein/AAA familyATPase

406924 406708 216 0.14 — — n.d.

All IGR transcripts identified by cDNA sequencing (sRNA and mRNAs) within a 400 kbp fragment of the chromosome (11.700–407.000) have been analyzedby northern hybridizations. Besides the genomic context and the length determined from cDNA sequencing and northern results, the respective differentialtranscription calculated from the normalized number of cDNA reads and from the northern analysis (normalized in respect to the 5S rRNA transcript level) aregiven. n.d., not detected.




Table S8. Nothern blot analysis of additional selected sRNA candidates

Strand IGR Transcript

Genomiccontext

orientation(1)

Function ofadjacent genes (1) 5’ end 3’ end �N score �N score

454regulation

Northern blotregulation

Transcriptlength

determined

� MM�3371/0001 asRNA001 443 Annotation/ Prog-nose/DipeptideABC transporter,binding protein

333 293 0.10 0.32 3.20 — n.d.

� MM�0052/53 asRNA047 434 Transposase/Hypo-thetical protein

70614 70782 0.40 1.20 3.00 0.95 160 bp

� MM�0117/18 sRNA009 444 Hypothetical pro-tein/CTP synthase

146550 146466 1.40 0.42 0.30 — n.d.

� MM�0124/25 sRNA012 343 Conserved protein/Universal stressprotein

154985 154889 0.35 1.10 3.14 — n.d.

� MM�0152/53 asRNA003 433 DNA integration/recombination/invertion protein/Conserved pro-tein

193140 193180 0.11 0.55 5.00 1.04 90, 50 bp

� MM�0173/74 sRNA016 343 AdoCbi amidohy-drolase CbiZ/Methanol corri-noid proteinMtaC3

231666 231559 6.00 35.00 5.83 1.22 130, 150 bp

� MM�0252/53 sRNA022 434 Conserved protein/Replication factorc subunit

336727 336912 0.40 1.60 4.00 1.02 130, 150 bp

� MM�0259/60 sRNA023 433 Dihydroxy-acid de-hydratase/Puta-tive SensoryTransduction pro-tein Kinase

347388 347497 0.65 2.50 3.85 0.89 90 bp

� MM�0402/03 sRNA030 433 Conserved protein/Hypothetical pro-tein similar to C-terminal domainof HdrB

515427 515497 0.70 5.00 7.14 1.03 70 bp

� MM�0666/67 sRNA041 344 Putative nickel-re-sponsive regula-tor NikR/Nitrore-ductase familyprotein

800086 799881 20.00 0.24 0.01 0.01 110, 120 bp

� MM�0699/700 sRNA045 334 Conserved protein/Vacuolar-typeH�-pyrophos-phatase

840527 840820 8.00 3.50 0.44 3.07 150, 200 bp

� MM�0701/02 sRNA047 343 Vacuolar-type H�-pyrophosphatase/Hypothetical per-mease

846629 846462 3.70 1.70 0.46 0.79 90 bp

� MM�0710/11 asRNA008 343 Transposase/Hypo-thetical protein

856744 856688 0.60 8.60 14.33 1.73 50 bp

� MM�0907/08 sRNA057 434 Hypothetical pro-tein/Conservedprotein

1073867 1074062 0.23 1.40 6.09 1.00 130, 150 bp

� MM�1072/73 asRNA011 343 Conserved protein/Methanol corri-noid proteinMtaC2

1260553 1260358 0.65 0.10 0.15 1.99 130, 180 bp

� MM�1072/73 sRNA066 333 Conserved protein/Methanol corri-noid proteinMtaC2

1261239 1261343 — 0.58 �R 1.17 331 bp




Genomiccontext

orientation(1)


454regulation


Transcriptlength

determined

� MM�1198/99 asRNA014 433 Transposase/Con-served protein

1425029 1425102 12.00 33.00 2.75 1.33 130, 300 bp

� MM�1432/33 spRNA15 434 Hypothetical pro-tein/Hypotheticalprotein

1714676 1714902 9.50 2.6 0.27 0.28 90, 110 bp

� MM�1502/03 sRNA158 433 S-adenosylmethi-onine synthetase/ATP phosphori-bosyltransferase

1792239 1792303 0.20 1.00 5.00 — n.d.

� MM�1716/17 sRNA087 443 Transcriptional reg-ulator, ArsR fami-ly/Conserved pro-tein

2060959 2060895 3.20 8.00 2.50 0.98 170, 190 bp

� MM�1721/22 sRNA089 443 Transcriptional reg-ulator, ArsR fami-ly/Hypotheticalprotein

2066165 2066098 1.10 3.80 3.45 1.00 65 bp

� MM�1732/33 sRNA090 443 Transcriptional reg-ulator, ArsR family/Me-talloproteinase

2075070 2074994 0.86 2.60 3.02 0.79 67 bp

� MM�1838/39 sRNA093 443 Ferredoxin/Con-served protein

2190331 2190268 0.14 1.20 8.57 1.04 63, 65, 130bp

� MM�1870/71 sRNA094 334 Conserved protein/Vanillate decar-boxylase protein

2223513 2223580 0.28 0.86 3.07 1.22 130, 242 bp

� MM�2025/26 sRNA099 343 Hypothetical pro-tein/Hypotheticalprotein

2419520 2419489 — 0.52 �R — n.d.

� MM�2098/99 spRNA28 444 Conserved protein/Hypothetical pro-tein

2506609 2506556 0.16 0.38 2.38 2.52 130 bp

� MM�2335/36 sRNA102 343 Conserved protein/Translation initia-tion factor 1A(EIF-1A)

2793547 2793474 0.14 0.56 4.00 0.52 130 bp

� MM�2368/69 sRNA159 343 Aspartate amino-transferase/Cyto-chrome c-typebiogenesis pro-tein

2825468 2825442 — 0.46 �R 0.10 100 bp

� MM�2375/76 asRNA028 344 Conserved protein/Conserved pro-tein

2833331 2833091 7.40 — �R 0.11 70, 130 bp

� MM�2390/91 asRNA044 434 Conserved protein/Transposase

2851716 2851779 0.11 0.35 3.18 0.81 63, 65 bp

� MM�2411/12 sRNA106 343 Hypothetical pro-tein/Conservedprotein

2873129 2873057 0.12 0.60 5.00 1.01 70 bp

� MM�2491/92 sRNA160 344 F420H2 dehydroge-nase, subunitA/Putative Ferre-doxin

2969755 2969933 — 0.35 �R 56.61 130 bp

� MM�2536/37 spRNA34 333 LSU ribosomal pro-tein L21E/Hypo-thetical protein

3023963 3024199 0.16 0.46 2.88 1.15 1100 bp

� MM�2655/56 sRNA118 334 Hypothetical pro-tein/Peptidyl-prolyl cis-transisomerase

3173527 3173664 1.40 — �R 1.48 75, 80 bp

� MM�2686/87 asRNA036 334 Transposase/Trans-posase

3210618 3210670 0.27 1.10 4.07 7.13 50 bp




Genomiccontext

orientation(1)


454regulation


Transcriptlength

determined

� MM�2797/98 sRNA124 343 Pirin/Conservedprotein

3356686 3356386 12.00 4.00 0.33 0.46 235, 310,360 bp

� MM�2807/08 sRNA126 334 Phosphoribosyl-formylglycinami-dine synthase/Conservedprotein

3370460 3370697 4.00 2.90 0.73 0.26 90, 100 bp

� MM�2950/51 sRNA132 443 Conserved protein/Hypothetical pro-tein

3556472 3556367 2.00 0.20 0.10 1.88 240 bp

� MM�3167/68 asRNA041 334 Transposase/Con-served protein

3851969 3852065 0.70 2.90 4.14 0.88 80 bp

� MM�3183/84 sRNA146 344 Ketoisovalerateoxidoreductasesubunit/Con-served protein

3871270 3871088 5.20 5.00 0.96 1.03 85, 90 bp

� MM�3337/38 sRNA154 443 Conserved protein/Hypothetical pro-tein

4065452 4065321 — 1.00 �R 18.03 80, 130 bp

sRNA candidates with significant transcript levels have been analyzed by Northern hybridization. Besides the length determined from cDNA sequencing andNorthern results, the respective differential transcription calculated from the normalized number of cDNA reads and from the Northern analysis (normalizedin respect to the 5S rRNA transcript level) are given. n.d., not detected.




Table S9. Northern blot probes used in this study

Northern blot probe Sequence (5�–3�)

MM0001-MM3371 CAG TTT GTC TTA AAA ATC TTT AAA AAA GTA

MM0052-MM0053 TGT GAC CTT GAT CAC GGA TGC

MM0118-MM0117a CCG GAG TCA TCC AGC AAA TG

MM0125-MM0124 GAA CGG GGT TTT TTG AAG GAG G

MM0152-MM0153 GTG CGA GAG GTG CGA TTC G

MM0259-MM0260 GCA GGC CCG TTC ACT ATG

MM0402-MM0403 CCC GAA CTC CAT AAA ATC TGC C

MM0666 CCC ATT TTT ACG TCT GTT CGC T-3’

MM0699-MM 0700 CGA TGG TTA TTT ATG TAT CGA ATT GC

MM0702-MM0701 GTT TCC CGC TCA CAT TAC TCA C

MM0711-MMZRNA046 AAT GAA CAT CAC AAA ACA TAG AGC C

MM0907-MM0908 GAC TTT AAT CCT CAC TTT TAC TGA ATT G

MM1072-MM1073 CTC CTT ATG TTG AGA CTC TAT CC

MM1073-MM1072 GTT TAA TTT ACA TTT CAA CGG TGA GTG

MM1198-MM1199 GTA TCG ACT CAG TTC CAA AAT CTA G

MM1502-MM1503 GTA ATT TAA TAG AAA CAG ACT ATC GTG TC

MM1716 CAA CCC TCC AGA GCA GAT TTG

MM1722-MM1721 CAC ATT TGA ACT TCA CAT GCC CTG

MM1733-MM1732 CAT ATT TGA ACT TCA CAT GCC CTG

MM1839-MM1838 GAA CCC CAC ATA CCC GAA G

MM1870-MMZRNA003 GGG AAT ACT ACT TTG AGA ACA CTT G

MM2026-MM2025 GTT AAA TTC ATA TAT TTG TGA ATT TAA ACT

MM2099-MM2098 AAT AAC CCA CCA GAC CCG TAT C

MM2336-MM2335 AAC ATG TTG AGC ACT GAA TTA TAC AAT TA

MM2369-MM2368 AAT TAA CCA ATT TCT GAA ATA GTT A

MM2376-MM2375 TGT CAG AAG GCA GCA GGA G

MM2390-MM2391 CTG TAT CCT TTT CCT TTC ACC AC

MM2412-MM2411 CCG AAC TCC ATA AAC GCG C

MM2491-MM2492 CTG CTT TCC AGA ATA TGA CAG CT

MM2536-MM2537 GGA GGT CAG CAT ACC TTA AAC

MM2655-MMZRNA042 CTG AAA ATC CGT TTT TCT GTT TTT CTG

MM2686-MM2687 TGA ACA TCA CAA AGC AGA GAG C

MM2798-MM2797 ACC CCA TTC AAT ATT AGC ATT TAG G

MM2807-MM2808 CTA AAT TTG TGT CTG TCG GGT AG

MM2951-MM2950 CCT GCC AGA AAT TTG AAT ACT TAC AC

MM3167-MM3168 TTC TTG GAG ATT TCT CTA CTT TGA C

MM3184-MM3183 GAT CCA ACC CGA AAT TGA GAG G

MM3338-MM3337 GAG GCT TTG ATT TAC TCG TAA GC

MMZRNA047-MM0253b CTA TGG AAA AGA GAC CCG CTC

MMZRNA066-MM0173 CCG AAG GCT CGC ACA CCC

MM0010-MM0011 GGA AGC ATG GAA TCT TAA CAT AAG C

MM0015-MM0016b GGT TTT TAA TAA CAG ATC ATA CGT CTC

MM0015-MM0016a CAC CTT GTT TTA GTT TTT GCT GTT TG

MM0017-MM0016 AAA GAC GCC TAA AAT CTA CAT TTT AC

MM0037-MM0038 GCT GTT AGC TGT CAA ATT TAC AGG

MM0039-MM0040 TTT CCA AAG ATA ATT TTC CCA ACT GC

MM0047-MM0046 CCT AAA AGG CTT ACA GCT ATT GC

MM0052-MM0053 TGT GAC CTT GAT CAC GGA TGC

MM0072-MM0071 CAA TTA TTA AAC TGA AAA AGA ATC CGG C

MM0077-MM0078 ATC ACG ATC CGG AGG TTC TC

MM0089-MM0090 GCT TAA GGC TGT GAA GGT ACC

MM0091-MM0090 AGA ATT CCC ATG CAA TGA TCA GTT G

MM0094-MM0093 GGA ACC TAG GGT AAA GTA CAA TG

MM0117-MM0118 CAT GAA CTT GAC TGG ATG CAT TTT G

MM0118-MM0117a CCG GAG TCA TCC AGC AAA TG

MM0118-MM0117b CCC CAG CAG ATA CCA CAT TAA C

MM0124-MM0125a ATC CAT CTG TCT TTC CTT TCT TGT

MM0124-MM0125b TGG TGA ACG GGC CAA GCT C

MM0125-MM0124 GAA CGG GGT TTT TTG AAG GAG G

MM0128-MM0129 CAT GTA AAA AAT ATC CTG C

MM0131-MM0130 CTG TCT CCC GAT CCA TAC TG

MM0132-MM0131 TTC TCA CAT TTA TTT TTA GAT AGT TTG AAG

MMZRAN037-MM0137 TAT TTG ATC CGG AAC AGG TTA TCT T

MM0151-MM0152 GAC AAC TTT GAG AAG CCT GCC



Northern blot probe Sequence (5�–3�)

MM0152-MM0153 GTG CGA GAG GTG CGA TTC G

MM0159-MM0160 TAC AAC TAT ATG TGT TCT TAA TTG ATA TAT

MMZRNA066-MM0173 CCG AAG GCT CGC ACA CCC

MM0179-MM0178 GGT CTG TTC GCA TTA GGG ATA G

MM0184-MM0183 CAG AAC CGT CAG ATG AGC TG

MM0189-MM0188 CCG GCG GTT TGT ATT CAA GC

MM0198-MM0199 AGT CCT CAA TTC CAT TAA TTT

MM0206-MM0207 ACT GAC TGG CCT CGT CTT TC

MM0251-MM0252 AAG CAA TCC TGC ACC CTG G

MMZRNA047-MM0253a CTT ACA AAA GAG AGA CCC GCT C

MMZRNA047-MM0253b CTA TGG AAA AGA GAC CCG CTC

MM0258-MM0257 CCA GTT TAC TGG CTT TGT CTT CT

MM0260-MM0259 AAT AAA AGG ATC ACA GTA AGG TAT C

MM0259-MM0260 GCA GGC CCG TTC ACT ATG

MM0263-MM0262 AGG CAA TAA TCC AGC TAG AAC T

MM0269-MM0268 CAC TCG AAT TGA TCC CTG GG

MM0303-MM0304 GTT TAG AAC CCG ACT GGA TAA ATG

MM0304-MM0303 CAT AAT CAT TTA TCC AGT CGG GTT C

MM0129-MM0128 AAT GCA CAG GAG AAT TTG CAG G

sRNA159-NB CAA TTA ACC AAT TTC TGA AAT AGT T

asRNA014-NB CTA TAA TTA TGT AAT GAT GTT ACG GC

asRNA044-NB CAC AAA AAA ACA GGA TGC AGA GTC

glnA1-NB CGT AAA CTG GGT ACG GAT AAA C



supporting information - pnas.org · 50 68049 68345 296 glutamyl-trna ... 93 120209 120111 98...

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