Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

Neuhaus, Klaus; Landstorfer, Richard; Fellner, Lea; Simon, Svenja; Schafferhans, Andrea; Goldberg, Tatyana; Marx, Harald; Ozoline, Olga N.; Rost, Burkhard; Kuster, Bernhard; Keim, Daniel A.; Scherer, Siegfried

doi:10.1186/s12864-016-2456-1

Table 1 Novel genes detected in EHEC

From: Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

Gene description						Ribosomal footprints^e			MS^h			PlatProm predictionⁱ
Name^a	Classification^b	Start^c	Stop^c	Length [bp]	Origin^d	RPKM	Gene coverage^f	Ribosomal coverage value^g (RCV)	LB	LB-Nit	LB-small	Upstream of start codon [bp]	Score
X001	real	217270	217488	219		1690	0.99	2.35				−460	9.00
X002 yahH	real	391261	391725	465		56	0.61	0.64				−211(yahF)	8.93
X003	real	570516	570710	195		102	0.72	0.69				--	--
X004	real	667557	667805	249		18	0.59	0.51	2		2	−287	7.90
X005	real	713269	713421	150		190	0.92	0.89				−54(cstA)	7.61
X006	real	713433	713630	198		166	0.86	0.77				−54(cstA)	7.61
X007*		790488	790682	195		79	0.65	0.80				−563	9.15
X008	real	902889	903083	195	phage	678	0.71	0.82				−14	7.63
X009*	real	978607	978747	141		17	0.52	0.50				−129	7.63
X010a	real	1112292	1112471	180		35	0.75	0.71				−297	8.28
X010b		1508079	1507899	duplicate of X010a
X011*	real	1146872	1147027	156		13	0.53	0.38				--	--
X012	real	1152583	1152795	213		57	0.51	0.42				−2	7.66
X013	real	1256680	1256967	288	phage	230	0.89	0.92			2	−590	7.73
X014a	real	1267635	1267820	186	phage	552	0.66	0.26				−67	8.07
X014b		2314896	2314711	duplicate of X014a
X015	real	1334776	1334931	156	phage	35	0.84	0.32				−70(trxB)	7.84
X016a	real	1346825	1347184	360	phage	58	0.65	0.69				−20	9.29
X016b		3000443	3000802	duplicate of X016a
X017	real	1353605	1353772	168	phage	23	0.52	0.21				−91	9.27
X018	real	1411438	1411557	120		49	0.8	0.37				−30	10.92
X019	real	1680779	1680967	189	phage	242	0.77	3.51				−269	9.01
X020	real	1772962	1773144	183		53	0.6	1.04				−24(dadA)	10.52
X021	real	1843458	1843622	165		1029	0.65	2.56				−625	7.74
X022*	real	1866296	1866505	210	phage	2169	0.82	0.73				−6	7.63
X023*		1866493	1866648	156	phage	280	0.88	1.30				−203	7.63
X024	real	1881598	1881819	222	phage	21	0.37	0.60	2	2	2	−76	8.93
X025a		1389500	1389288	duplicate of X015b
X025b	real	1888594	1888806	213	phage	524	0,95	0,08				−112	8,27
X026	real	1905731	1905850	120	phage	622	0.7	1.01				−77(Z2121)	12.18
X027	real	2038161	2038382	222		75	0.51	1.46				−313	7.47
X028*		2101101	2101247	147		131	0.61	1.70				0	8.00
X029	real	2109655	2109921	267		629	0.97	0.85				--	--
X030	real	2138823	2139137	315	phage	1520	0.98	1.35				−53	16.96
X031	real	2168349	2168567	219		77	0.66	0.60				−110	8.48
X032a		1269797	1269913	duplicate of X032c
X032b		1868589	1868705	duplicate of X032c
X032c	real	2312618	2312734	117		650	0.81	0.74				−447	7.83
X033*		2379507	2379659	153		348	0.87	1.50				−77	12.26
X034	real	2430386	2430598	213		47	0.53	0.22				−9	11.59
X035*		2480019	2480177	159		25	0.52	0.20				−63	10.51
X036	real	2584677	2584847	171		52	0.66	0.17				−162	12.18
X037	real	2663871	2664122	252		14	0.53	0.58				−243	12.65
X038	real	2670869	2671075	207	phage	1209	0.8	0.69				−28	11.39
X039	real	2742703	2742918	216		90	0.58	0.61				−103	7.60
X040	real	2777135	2777347	213	phage	37	0,57	0,02				--	--
X041	real	2779284	2779508	225	phage	57	0.73	1.32				--	--
X042	real	2844454	2844606	153		768	0.84	0.83				−295(X043)	8.26
X043	real	2844640	2844804	165		212	0.92	0.44				−295	8.26
X044	real	2844865	2845074	210		36	0.53	0.17				−210	11.00
X045	real	2845149	2845358	210		163	0.9	0.16				−23	9.54
X046*		2845408	2845602	195		145	0.69	0.35				−33	9.54
X047	real	2966787	2966987	201	phage	34	0.71	0.17				−21	8.08
X048	real	3003688	3003945	258	phage	40	0.65	1.96				−353	8.18
X049	real	3004951	3005067	117	phage	241	0.75	1.39		3	2	−93	9.71
X050	real	3013440	3013694	255	phage	28	0.64	0.47				−71(Z3371)	8.46
X051	real	3261588	3261758	171		89	0.86	0.35				--	--
X052*		3271689	3271820	132		34	0.79	0.32				−95	9.93
X053 suhB	real	3453780	3454583	804		41	0.53	0.20	9	13	2	−36	9.48
X054*		3894853	3894993	141		98	0.86	0.56				−220	8.25
X055	real	3918141	3918344	204		47	0.56	0.31				--	--
X056	real	4207372	4207641	270		725	0.92	0.66				−52	10.58
X057	real	4240665	4240883	219		2974	0.88	2.01				−24	13.80
X058*		4441485	4441643	159		359	0.98	0.64				−569	9.75
X059	real	4449723	4449821	99		19	0.6	0.08				−96	7.97
X060	real	4468299	4468592	294		639	0.84	2.99				−253	9.57
X061	real	4585965	4586174	210		202	0.92	1.98		2	2	−67	9.03
X062	real	4654347	4654490	144	phage	29	0.73	0.89				−393	8.17
X063*		4730352	4730537	186		15	0.51	0.95				−533	11.48
X064	real	4793504	4793737	234		20	0.53	0.28				--	--
X065	real	4870817	4870978	162		38	0.74	1.28				−90(pldA)	8.1
X066*		4873916	4874122	207		117	0.84	2.58				−104	7.92
X067	real	4916583	4916756	174		162	0.84	0.64				−22(yihI)	11.84
X068*		5077694	5077831	138		2040	0.97	0.55				−368(nfi)	7.61
X069	real	5369765	5369998	234		141	0.94	0.33				−159(pepA)	11.47
X070	real	5456776	5457042	267		53	0.52	3.58				−163(yjiM)	8.02
X071	real	5494158	5494394	237		45	0.57	2.82				−27	8.35
X072	real	5515374	5515541	168		38	0.69	0.80				−39(serB)	7.9

^a The asterisk indicates genes not annotated in any other organism (blastp against GenBank, threshold E-value ≤10⁻¹⁰)
^b Machine learning classification based on the set of annotated proteins (“real”) and their shuffled counterparts as training set
^c The positions are given in relation to GenBank accession no. NC_002655, the original genome sequence of strain EDL933. Only very recently, the genome has been updated (GenBank accession no. CP008957)
^d Genes originating from prophages are indicated
^e The RPKM footprint and coverage of the actual ORF with footprints is given as average of two replicate experiments for bacteria grown in LB medium
^f Fraction of the ORF covered with one or more footprint reads
^g Ratio of RPKM footprints to RPKM transcriptome
^h Indicated is the number of individual peptide spectra gained by mass spectrometry
ⁱ Putative promoters have been predicted using PlatProm. The position of the assumed transcription start site upstream of the start codon and the quality of the prediction (score) are given

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