Additional File 8 — 6S RNA evidence in Weissella

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Additional File 8 — 6S RNA evidence in Weissella

Supplemental Figure 1: Genomic context of rarA in Weissella koreensis and Weissella confusa mapped RNA- Seq data from bioprojects PRJNA306639 and PRJNA532838. The number of mapped reads is indicated on the right. Conditions are overlayed in different colors. As for main Figure 2, putative Rho-independent terminators are indicated by red hexagons. Genes in close proximity (<20 nt) are indicated by a semicircle connecting them. The data verifies active transcription of the predicted 6S RNA inW. koreensis. No prediction was found forW. confusa.

However, similar transcriptional activity is observed for the expected locus immediately downstream ofrarA.

ar NAD

lmwppp

hp.8 pcrf3 rarA acy ptsadcp

6S* hp.3

uspA gbpAtAbp

NC_015759.1

-5000 -2500 0 2500 5000

gene

6S*: predicted 6S RNA acy: acyltransferase ar: aldo/keto reductase

gbpAtAbp: glycine betaine/L-proline ABC transporter ATP-binding protein hp.3: hypothetical protein #3

hp.8: hypothetical protein #8

lmwppp: low molecular weight phosphotyrosine protein phosphatase NAD: NAD(P)-dependent oxidoreductase

pcrf3: peptide chain release factor 3

ptsadcp: prolyl-tRNA synthetase associated domain-containing protein rarA: replication-associated recombination protein A uspA: universal stress protein

day 7 (168M unique mapped reads) day 13 (408M unqiue mapped reads) day 18 (174M unique mapped reads) day 25 (189M unique mapped reads) PRJNA306639

Metatranscriptome from kimchi microbiome Weissella koreensis KACC 15510 (GCF_000219805.1, ASM21980v1)

(0≙332813, -, NC_015759.1)

0 500 1000 3000 3500

2500 2000 1500

DUF402 hp.8 pcrf3

hp.6 DUF1694 rarA

hp.3

uspA hp.9

tL

NZ_JQAY01000004.1

-5000 -2500 0 2500 5000

gene DUF1694: DUF1694 domain-containing protein DUF402: DUF402 domain-containing protein

hp.3: hypothetical protein #3 hp.6: hypothetical protein #6

hp.8: hypothetical protein #8 hp.9: hypothetical protein #9

pcrf3: peptide chain release factor 3

rarA: replication-associated recombination protein A

tL: tRNA-Lys uspA: universal stress protein

0 1000 2000 3000 4000 5000 6000 7000 8000 Weissella confusa (GCF_001436895.1, ASM143689v1) 9000

(0≙57247, -, NZ_JQAY01000004.1)

PRJNA532838

Transcriptome analysis of Weissella confusa XU1 grown in MRS broth in which the sole carbon source was:

Xylose (1430M - 1520M unique mapped reads) Glucose (1450M - 1520M unique mapped reads) Xylooligosaccharides

(1260M - 1420M unique mapped reads)

6S*

expected 6S RNA locus

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DUF402 hp.8 pcrf3 hp.6 DUF1694 rarA hp.19hp.3 uspA Lp vtl

NZ_CP007588.1

-5000 -2500 0 2500 5000

gene

DUF1694: DUF1694 domain-containing protein DUF402: DUF402 domain-containing protein hp.19: hypothetical protein #19

hp.3: hypothetical protein #3 hp.6: hypothetical protein #6 hp.8: hypothetical protein #8

Lp: Lysine permease pcrf3: peptide chain release factor 3 rarA: replication-associated recombination protein A

uspA: universal stress protein vtl: valine--tRNA ligase

Weissella ceti (GCF_000732905.1, ASM73290v1) (0≙1028355, -, NZ_CP007588.1)

hp.11 pcrf3 hp.6 DUF1694 hp.15 rarA hp.3 uspA hp.14 hp.10 csp

NZ_CP012873.1

-5000 -2500 0 2500 5000

gene

csp: cell surface protein DUF1694: DUF1694 domain-containing protein hp.10: hypothetical protein #10

hp.3: hypothetical protein #3 hp.6: hypothetical protein #6 pcrf3: peptide chain release factor 3

rarA: replication-associated recombination protein A uspA: universal stress protein

Weissella cibaria (GCF_001308145.2, ASM130814v2) (0≙1033256, +, NZ_CP012873.1)

DUF402 hp.8 pcrf3 hp.6 DUF1694 rarA hp.3 uspA hp.9 hemolysin III

NZ_ATUU01000002.1

-5000 -2500 0 2500 5000

gene

DUF1694: DUF1694 domain-containing protein DUF402: DUF402 domain-containing protein hemolysin III: hemolysin III

hp.9: hypothetical protein #9 pcrf3: peptide chain release factor 3 rarA: replication-associated recombination protein A

uspA: universal stress protein vtl: valine--tRNA ligase

Weissella halotolerans DSM 20190 (GCF_000420365.1, ASM42036v1) (0≙42354, -, NZ_ATUU01000002.1)

DUF402 pcrf3 hp.6 krfp DUF1694 rarA hp.3 uspA hp.9 hp.18 hemolysin III

NZ_CP014332.1

-5000 -2500 0 2500 5000

gene

hp.9: hypothetical protein #9 krfp: ketopantoate reductase family protein pcrf3: peptide chain release factor 3

Weissella jogaejeotgali (GCF_001932615.1, ASM193261v1) (0≙1585075, -, NZ_CP014332.1)

hp hp lmwppp hp.8 pcrf3 rarA acy 6S* hp.3 uspA hp.9 hp.18

NZ_JQBP01000001.1

-5000 -2500 0 2500 5000

gene

6S*: putative 6S acy: acyltransferase hp: hypothetical protein

hp.9: hypothetical protein #9

lmwppp: low molecular weight phosphotyrosine protein phosphatase pcrf3: peptide chain release factor 3

Weissella kandleri (GCF_001438705.1, ASM143870v1) (0≙31809, +, NZ_JQBP01000001.1)

Supplemental Figure 2: Genomic context ofrarAin furtherWeissella species. For each species, one representative strain is shown. Typically,rarAis followed by an intergenic region that is closed by a Rho-independent terminator.

In three species, a low-scoring 6S RNA candidate was predicted in this locus (highlighted in red). We assume that a similar transcript is produced from the remaining intergenic regions of the other species.

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DUF402 hp.8 pcrf3 hp.6DUF1694 rarA 6S* hp.3 uspA hp aat

NZ_JQCD01000018.1

-5000 -2500 0 2500 5000

gene

6S*: putative 6S aat: amino acid transporter DUF1694: DUF1694 domain-containing protein

DUF402: DUF402 domain-containing protein hp: hypothetical protein hp.3: hypothetical protein #3

rarA: replication-associated recombination protein A uspA: universal stress protein vtl: valine--tRNA ligase

Weissella minor (GCF_001437425.1, ASM143742v1) (0≙85550, +, NZ_JQCD01000018.1)

csp NUDIX hp 5mn DUF1694 rarA hp.3 uspA ABC ABC hp.9

NZ_DF820486.1

-5000 -2500 0 2500 5000

gene

5mn: 5'-methylthioadenosine/adenosylhomocysteine nucleosidase ABC: ABC transporter ATP-binding protein

ABC: ABC transporter permease

csp: cold-shock protein

DUF1694: DUF1694 domain-containing protein hp: hypothetical protein

hp.3: hypothetical protein #3 hp.9: hypothetical protein #9 NUDIX: NUDIX hydrolase

Weissella oryzae SG25 (GCF_000691805.2, ASM69180v2) (0≙139350, -, NZ_DF820486.1)

DUF402 pcrf3 hp.6 krfp DUF1694 rarA hp.3 uspA hp.9 hp.18 hemolysin III

NZ_CP023501.1

-5000 -2500 0 2500 5000

gene

hp.9: hypothetical protein #9 krfp: ketopantoate reductase family protein pcrf3: peptide chain release factor 3

Weissella paramesenteroides (GCF_002386265.1, ASM238626v1) (0≙243024, +, NZ_CP023501.1)

ATP tIpk Lpbdcp DUF1694 rarA hp.3 uspA hp.9 hp.18 hemolysin III

NZ_QRAS01000004.1

-5000 -2500 0 2500 5000

gene

ATP: ATP-dependent DNA helicase DUF1694: DUF1694 domain-containing protein hemolysin III: hemolysin III

Lpbdcp: LysM peptidoglycan-binding domain-containing protein rarA: replication-associated recombination protein A srfrE: septation ring formation regulator EzrA

tIpk: type I pantothenate kinase uspA: universal stress protein

Weissella soli (GCF_003353445.1, ASM335344v1) (0≙42927, +, NZ_QRAS01000004.1)

DUF402 hp.8 pcrf3 hp.6DUF1694 rarA 6S* hp.3 uspA hp.9 aat

NZ_LT907932.1

-5000 -2500 0 2500 5000

gene

6S*: putative 6S aat: amino acid transporter DUF1694: DUF1694 domain-containing protein

DUF402: DUF402 domain-containing protein hp.3: hypothetical protein #3 hp.6: hypothetical protein #6

rarA: replication-associated recombination protein A uspA: universal stress protein vtl: valine--tRNA ligase

Weissella viridescens (GCF_900216215.1, MFPC16A2805a-v1) (0≙575554, -, NZ_LT907932.1)

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Supplemental Figure 3: Structural alignment of predicted 6S RNAs inWeissellaspecies. W. confusawas predicted only based on RNA-Seq data (see Supplemental Figure 3 above).

...(((((((((.((.(((((((...((((..((((((((...((

kandleri A-AUUACCUGGUCGUACGCGUGAUUCAUAAUAUCAUAAUGUUGCUUUACAAC---UUUCU 56 koreensis AAAUUUCUUGGACGUACGCGUGAUCC-UAUAUUCAUUAUGUUGCUUUACAACCUUUUUCU 59 koreensis_KACC AAAUUUCUUGGACGUACGCGUGAUCC-UAUAUUCAUUAUGUUGCUUUACAACCUUUUUCU 59 confusa ----UCCUUGGACGUACGCAUGAUUCCUACUA-UAUGUAGUUGCUUUACAACCAUAU--U 53 viridescens AAAUUCCUUGAACAUACGCGUGAUUC-AAUUAUCUA-AAGUUGCUUUACAA--AUUUUCG 56 minor GAAUUCCUUGAACAUACGCGUGGUUC-UAUUAUCUA-AAGUUGCUUUACACUAAUUUUCG 58

...10...20...30...40...50...

((..(((((.((.((((((.(((((.(((.((((((...)))))))))...) kandleri AAACGGGAAUGGCGGAAAGCCGGCGGAGCAUGCCAU-GAC---AUGUGGUAGCGACAAAC 112 koreensis AAACGGGAAUGGCGGAAAGCCGGCGGAGCAUACCUU-AAC---ACGAGGUAGCUCCAAAU 115 koreensis_KACC AAACGGGAAUGGCGGAAAGCCGGCGGAGCAUACCUU-AAC---ACGAGGUAGCUCCAAAU 115 confusa GACCGGGGAUGUCGGGAAGCCGGCGAGGCAAGCUAU-UUC---ACUUAGUAGCCGCUAAA 109 viridescens AA-UGGGGAUGUCGGGAAGCCGGCGGGGCAUGCCAACCAAUGCUGUUGGAAGUCGUUAAC 115 minor AA-UGGGGAUGUCGGGAAGCCGGCGGGGCACGCCAACUACG--GGUUGGAAGCCGUCAAC 115

...70...80...90...100...110...

)))).)))...))))).)).)))....))))))).))))).)))).)))))).)...) kandleri GCUGUCUUAGU-GCCCACUUU-CUUAUA-CUAGGAGCCAACU-UUGACGAAUCAUCUAAC 168 koreensis GCUGUCUUAGU-ACCCACUUU-CUUAUC-UUAGGAGCCAACA-AUGACGGAUCAACUAAC 171 koreensis_KACC GCUGUCUUAGU-ACCCACUUU-CUUAUC-UUAGGAGCCAACA-AUGACGGAUCAACUAAC 171 confusa GCUGACUUAUUCACCCACUUA-CCUAUAAUCUGGAGUCAACUCAUUGUGAAUCG-UUAAC 167 viridescens GCUGACUUAUUCACCCACCUUUGCCA----UCGAAGCCAUCU-UAGACGAAUCAUCUAAC 170 minor GCUGACUUAUUCACCCACCUUUGCCA----UCGAAGCCGACU-UAGACGAAUCAUCUAAC 170

...130...140...150...160...170...

))))))...))))...

kandleri GGCGACAUACAAGUUUU---UU 187 koreensis GGCGCCAAUCAAGUGUUU---AC 191 koreensis_KACC GGCGCCAAUCAAGUGUUU---AC 191 confusa GGCGCCAAUCAAGUGUUCGUGCGCUACCACGGUU 201 viridescens GGUGUUAUACAAGUGUUU---AC 190 minor GGUGUUAUACAAGUGUUC---GU 190

...190...200...210..

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