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Listeria monocytogenes non-coding RNA

{{Infobox rfam

| Name = Listeria snRNA rli22

| image = RF01457.png

| width = 200

| caption = Predicted secondary structure of Listeria snRNA rli22

| Symbol = rli22

| AltSymbols =

| Rfam = RF01457

| miRBase =

| miRBase_family =

| RNA_type = gene, snRNA

| Tax_domain = Listeria

| CAS_number =

| EntrezGene =

| HGNCid =

| OMIM =

| PDB =

| RefSeq =

| Chromosome =

| Arm =

| Band =

| LocusSupplementaryData =

}}

Listeria monocytogenes is a gram positive bacterium and causes many food-borne infections such as Listeriosis. This bacteria is ubiquitous in the environment where it can act as either a saprophyte when free living within the environment or as a pathogen when entering a host organism. Many non-coding RNAs have been identified within the bacteria genome where several of these have been classified as novel non-coding RNAs and may contribute to pathogenesis.{{cite journal |vauthors=Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P |title=Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets |journal=Nucleic Acids Res. |volume=35 |issue=3 |pages=962–974 |year=2007 |pmid=17259222 |pmc=1807966 |doi=10.1093/nar/gkl1096 }}

Tiling arrays and mutagenesis identified many non-coding RNAs within the L. monocytogenes genome and the location of these non-coding RNAs within the bacterial genome was confirmed by RACE (rapid amplification of cDNA ends) analysis. These studies showed that the expression of many non-coding RNAs was dependent on the environment and that several of these non-coding RNAs act as cis-regulatory elements. Comparisons between previously characterized non-coding RNAs and those present in the L. monocyotogenes genome identified 50 novel non-coding RNAs in L. monocyotogenes. An additional comparative study between the pathogenic L. monocytogenes strain and the non pathogenic L. innocua strain identified several non-coding RNAs that are only present within L. monocytogenes which suggests that these ncRNAs may have a role in pathogenesis.{{cite journal |vauthors=Toledo-Arana A, Dussurget O, Nikitas G, etal |title=The Listeria transcriptional landscape from saprophytism to virulence |journal=Nature |volume=459 |issue=7249 |pages=950–956 |date=June 2009 |pmid=19448609 |doi=10.1038/nature08080 }} The tables below summarizes the location, flanking genes and also the characteristics of the novel small non-coding RNAs identified and the previously characterized non-coding RNAs present in L. monocytogenes

Novel Non-coding RNAs

class="wikitable"
ID

! Start

! Stop

! Size

! 5′ flanking gene

! sense of the gene on the genome

!a

!

! 3′ flanking gene

! Characteristic

! Rfam

rli22

| 31997

| 32107

| 110

| lmo0028

| ->

| ->

| ->

| lmo0029

| sRNA

|

rli23

| 172171

| 172268

| 97

| lmo0172

| <-

| ->

|

|

| sRNA Antisense to lmo0172 transposase Homolog of rli25 and rli35.

|

rli24

| 271029

| 271186

| 157

| lmo0256

| ->

| ->

| ->

| lmo0257

| sRNA

|

rli25

| 357618

| 357516

| 102

| lmo0330

| ->

| <-

|

|

| sRNA Antisense to lmo0330: transposase. Homolog of rli23 and rli35

|

rli26

| 388707

| 388520

| 187

| lmo0360

| ->

| <-

| <-

| lmo0361

| sRNA

|

rli27

| 434831

| 434929

| 98

| lmo0411

| <-

| ->

| <-

| lmo0412

| sRNA

|

rli28

| 507394

| 507206

| 188

| lmo0470

| ->

| <-

| ->

| lmo0471

| sRNA Homolog of rli50

|

rli29

| 507643

| 507450

| 193

| lmo0470

| ->

| <-

| ->

| lmo0471

| sRNA Antisense to the 5'UTR of lmo0471

|

rli30

| 540785

| 540670

| 115

| lmo0506

| ->

| <-

|

|

| sRNA Antisense to lmo0506

|

rli31

| 597812

| 597926

| 114

| lmo0558

| <-

| ->

| ->

| lmo0559

| Required for lysozyme resistance and pathogenesis.{{cite journal |vauthors=Burke TP, Loukitcheva A, Zemansky J, Wheeler R, Boneca IG, Portnoy DA |title=Listeria monocytogenes is resistant to lysozyme through the regulation, not the acquisition, of cell wall-modifying enzymes |journal=J. Bacteriol. |volume=196 |issue=21 |pages=3756–3767 |year=2014 |pmid=25157076 |pmc=4248804 |doi=10.1128/JB.02053-14 }} Structure characterized as two long hairpins. Interacts with the RNA binding global regulator SpoVG.{{cite journal |vauthors=Burke TP, Portnoy DA |title=SpoVG Is a Conserved RNA-Binding Protein That Regulates Listeria monocytogenes Lysozyme Resistance, Virulence, and Swarming Motility |journal=mBio |volume=7 |issue=2 |year=2016 |pmid=27048798 |pmc=4959528 |doi=10.1128/mBio.00240-16 }}

|

rli32

| 600750

| 600604

| 147

| lmo0560

| <-

| <-

| <-

| lmo0561

| sRNA

|

rli33

| 708326

| 708860

| 534

| lmo0671

| ->

| ->

| ->

| lmo0672

| sRNA

|

rli34

| 803031

| 802948

| 83

| lmo0777

| ->

| <-

| ->

| lmo0778

| sRNA

|

rli35

| 855495

| 855393

| 102

| lmo0828

| ->

| <-

|

|

| sRNA Antisense to lmo0828: transposase. Homolog of rli23 and rli25

|

rli36

| 859527

| 859444

| 83

| nifJ

| ->

| <-

| <-

| fbp

| sRNA

|

rli37

| 907576

| 907832

| 256

| lmo0866

| ->

| ->

| ->

| lmo0867

| ORF ORF of 58aa. RBS region: TGATACGGGAGTGTGGTGCTAGTTATG

|

rli38

| 1152549

| 1152917

| 369

| lmo1115

| <-

| ->

| ->

| lmo1116

| sRNA role in virulence

|

rli39

| 1179807

| 1179993

| 187

| lmo1149

| ->

| ->

| <-

| lmo1150

| sRNA Annotated as a cobalamin riboswitch in Rfam

|

rli40

| 1275810

| 1275547

| 264

| lmo1251

| ->

| <-

| <-

| lmo1252

| ORF ORF of 64 aa. RBS region: AGTGAGGCGTCCTTATG

|

rli41

| 1277207

| 1276713

| 495

| lmo1252

| <-

| <-

| ->

| lmo1253

| Two ORFs ORF of 45 aa. RBS region: AGAGGAGGTATTTTCTATG ORF of 35 aa. RBS region:AAGGAGGAAAACAAATTG

|

rli42

| 1399617

| 1399447

| 171

| lmo1374

| ->

| <-

| ->

| lmo1375

| sRNA

|

rli43

| 1861630

| 1861377

| 253

| inlC

| <-

| <-

| <-

| rplS

| ORF ORF of 35aa. RBS region: AGAGTGAGGTGTAATATG

|

rli44

| 2039087

| 2039375

| 289

| lmo1964

| <-

| ->

| <-

| lmo1965

| ORF ORF of 28aa. RBS region: GGAAAGGATAACCCATG

|

rli45

| 2154775

| 2154852

| 77

| lmo2074

| ->

| ->

| <-

| lmo2075

| sRNA Antisense to rli46

|

rli46

| 2155058

| 2154765

| 294

| lmo2074

| ->

| <-

| <-

| lmo2075

| sRNA Antisense to rli45

|

rli47

| 2226024

| 2226532

| 508

| lmo2141

| ->

| ->

| <-

| lmo2142

| sRNA

|

rli48

| 2361423

| 2361274

| 149

| lmo2271

| <-

| <-

| ->

| lmo2272

| sRNA

|

rli49

| 2660179

| 2660364

| 185

| lmo2579

| ->

| ->

| <-

| lmo2580

| sRNA

|

rli50

| 2783274

| 2783098

| 176

| lmo2709

| ->

| <-

| <-

| lmo2710

| sRNA Homolog of rli28

|

rli51

| 207589

| 207709

| 120

| hly

| ->

| ->

| ->

| mpl

| 5′-UTR-derived Increased in intestinal lumen

|

rli52

| 552421

| 552327

| 94

| lmo0517

| <-

| <-

| <-

| lmo0518

| 5′-UTR-derived Putative riboswitch.

|

rli53

| 955829

| 956001

| 172

| lmo0918

| ->

| ->

| ->

| lmo0919

| 5′-UTR-derived Putative riboswitch.

|

rli54

| 1078584

| 1079111

| 527

| lmo1051

| <-

| ->

| ->

| pdhA

| 5′-UTR-derived Putative riboswitch.

|

rli55

| 1198107

| 1198389

| 282

| lmo1170

| ->

| ->

| ->

| pduQ

| 5′-UTR-derived Putative riboswitch.

|

rli56

| 1199859

| 1199958

| 99

| pduQ

| ->

| ->

| ->

| lmo1172

| 5′-UTR-derived Putative riboswitch.

|

rli57

| ?

| 1216658

| ?

| lmo1190

| ->

| ->

| ->

| cbiA

| 3′-UTR-derived Annotated as a cobalamin riboswitch in Rfam lmo1190-rli57 transcript levelncreasedinintestinal lumen

|

rli58

| ?

| 1639974

| ?

| rpsD

| ->

| <-

| <-

| lmo1597

| 3′-UTR-derived |

|

rli59

| 1702553

| 1702373

| 180

| lmo1652

| <-

| <-

| <-

| lmo1653

| 5′-UTR-derived

|

rli60

| 2054124

| 2054308

| 184

| lmo1982

| <-

| ->

| ->

| ilvD

| 5′-UTR-derived Putative riboswitch.

|

rli61

|2275363

|2275258

|106

|lmo2187

|<-

|<-

|<-

|lmo2188

|5′-UTR-derived Putative riboswitch

|

rli62

|2364508

|2364337

|172

|lmo2277

|<-

|<-

|<-

|lmo2278

|5′-UTR-derived Putative riboswitch.

|

rli63

|2613301

|?

|?

|atpI

|<-

|<-

|<-

|lmo2537

|5′-UTR-derived Putative riboswitch

|

rliA

|513584

|513807

|224

|lmo0476

|<-

|>-

|>-

|lmo0477

|snRNA

|

rliB

|544357

|544716

|360

|lmo0509

| ->

| ->

| ->

|lmo0510

|sRNA

|

rliC

|1154309

|1154671

|363

|lmo1117

|->

|->

|<-

|lmo1118

|sRNA

|

rliD

|1359529

|1359202

|328

|rpsO

| ->

| <-

| ->

|pnpA

|sRNA antisense

|

rliE

|1584586

|1584808

|223

|comC

| <-

| ->

| <-

|folC

|sRNA antisense to comC mRNA

|

rliF

|2106292

|2106073

|220

|nadA

| ->

| <-

| <-

|lmo2026

|snRNA

|

rliG

|2386992

|2386715

|278

|lmo2302

| <-

| <-

| <-

|lmo2303

|sRNA

|

rliH

|1180826

|1181254

|429

|lmo1150

| <-

| ->

| ->

|lmo1151

|sRNA antisense

|

rliI

|2842200

|2841962

|239

|lmo2760

| <-

| <-

| ->

|lmo2761

|sRNA

|

sbrA{{cite journal |doi=10.1128/JB.00740-08 |vauthors=Nielsen JS, Olsen AS, Bonde M, Valentin-Hansen P, Kallipolitis BH |title=Identification of a sigma B-dependent small noncoding RNA in Listeria monocytogenes. |journal=J Bacteriol |volume=190 |issue=18 |pages=6264–6270 |year=2008 |pmid=18621897 |pmc=2546787}}

| 1399363

| 1399433

| 70

|lmo1374

| ->

| ->

| ->

|lmo1375

| sRNA

aArrows indicate the sense of the gene on the genome. Bold arrows indicate gene absent from L. innocua.

Listeria monocytogenes EGD-e strain was used in these studies EMBL accession AL591824.1

Characterised non-coding RNAs

style="background: transparent;"
style="vertical-align: top;"

|

{| class="wikitable"

! ID !! Rfam

SAMRF00162
LhrCRF00616
TPPRF00059
glmSRF00234
PreQ1RF00522
T-boxRF00230
SsrSRF00013

|

class="wikitable"

! ID !! Rfam

LhrBRF00558
FMNRF00050
ssrARF00023
SRPRF00169
PrfARF00038
L10 leaderRF00557
PurineRF00167

|

class="wikitable"

! ID !! Rfam

lysineRF00168
yybP-ykoYRF00080
glycineRF00504
L21RF00559
RyrRRF00515
LhrARF00615
L13RF00555

|}

References

{{reflist}}

External links

  • [https://archive.today/20121205022142/http://rfam.org/ Rfam database]

{{Listeria|state=expanded}}

{{Navbox

| name = hidden

| title = Gallery of secondary structure images

| titlestyle = background:#e7dcc3

| state = collapsed

| list1 = {{Gallery

| Image:RF01457.png|Listeria snRNA rli22: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01457 RF01457].

| Image:RF01458.png|Listeria snRNA rli23: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01458 RF01458].

| Image:RF01459.png|Listeria snRNA rliE: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01459 RF01459].

| Image:RF01460.png|Listeria snRNA rliH: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01460 RF01460].

| Image:RF01461.png|Listeria snRNA rli24: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01461 RF01461].

| Image:RF01462.png|Listeria snRNA rli26: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01462 RF01462].

| Image:RF01463.png|Listeria snRNA rli27: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01463 RF01463].

| Image:RF01464.png|Listeria snRNA rliA: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01464 RF01464].

| Image:RF01465.png|Listeria snRNA rli31: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01465 RF01465].

| Image:RF01466.png|Listeria snRNA rli34: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01466 RF01466].

| Image:RF01467.png|Listeria snRNA rli36: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01467 RF01467].

| Image:RF01468.png|Listeria snRNA rli32: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01468 RF01468].

| Image:RF01469.png|Listeria snRNA rli33: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01469 RF01469].

| Image:RF01470.png|Listeria snRNA rli38: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01470 RF01470].

| Image:RF01471.png|Listeria snRNA rliB: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01471 RF01471].

| Image:RF01472.png|Listeria snRNA rli40: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01472 RF01472].

| Image:RF01473.png|Listeria snRNA rli41: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01473 RF01473].

| Image:RF01474.png|Listeria snRNA rli42: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01474 RF01474].

| Image:RF01475.png|Listeria snRNA rli45: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01475 RF01475].

| Image:RF01476.png|Listeria snRNA rliF: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01476 RF01476].

| Image:RF01477.png|Listeria snRNA rli43: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01477 RF01477].

| Image:RF01478.png|Listeria snRNA rli47: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01478 RF01478].

| Image:RF01479.png|Listeria snRNA rli48: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01478 RF01479].

| Image:RF01480.png|Listeria snRNA rli52: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01480 RF01480].

| Image:RF01481.png|Listeria snRNA rli53: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01481 RF01481].

| Image:RF01482.png|Listeria snRNA rli55: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01482 RF01482].

| Image:RF01483.png|Listeria snRNA rli56: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01483 RF01483].

| Image:RF01484.png|Listeria snRNA rli59: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01484 RF01484].

| Image:RF01485.png|Listeria snRNA rli61: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01485 RF01485].

| Image:RF01486.png|Listeria snRNA rli62: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01486 RF01486].

| Image:RF01487.png|Listeria snRNA rliI: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01487 RF01487].

| Image:RF01488.png|Listeria snRNA rli49: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01488 RF01488].

| Image:RF01489.png|Listeria snRNA sbrA: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01489 RF01489].

| Image:RF01490.png|Listeria snRNA rli51: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01490 RF01490].

| Image:RF01491.png|Listeria snRNA rli54: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01491 RF01491].

| Image:RF01492.png|Listeria snRNA rli28: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01492 RF01492].

| Image:RF01493.png|Listeria snRNA rli37: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01493 RF01493].

| Image:RF01494.png|Listeria sRNA rliD: Predicted secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF01494 RF01494].

|}}

}}

Category:Listeriaceae

Category:Non-coding RNA