Regulatory sequences involved in the translation of Neurospora crassa mRNA: Kozak sequences and stop codons


We have analyzed the sequences of 77 nuclear genes of N. crassa thought to be transcribed by RNA polymerase II (References 1-72) which should represent virtually all of the presently published nuclear gene sequences for this fungus. 

Regulatory sequences involved in the translation of Neurospora crassa mRNA: Kozak sequences and stop codons

Jon J.P. Bruchez, J. Eberle and V.E.A. Russo -Max Planck Institut für Molekulare Genetik, Ihnestraße 73, D-14195 Berlin, Germany 
We have analyzed the sequences of 77 nuclear genes of N. crassa thought to be transcribed by RNA polymerase II (References 1-72) which should represent virtually all of the presently published nuclear gene sequences for this fungus. Kozak (1988, Nucl. Acids Res. 15:8125-) analyzed 699 vertebrate genes leading to identification of the vertebrate consensus sequence for initiation of translation, or Kozak Sequence: 
G44C39C53(A61/G36)(C49/A27)C55A100T100G100G46
We show here that the N. crassa Kozak sequence is: 
C57NNNC77A81(A44/C43)"T"3A99T100G99G51C53
where the subscript number indicates the % occurrence of the particular nucleotide and "T" indicates the conserved absence of that particular nucleotide. 
We arbitrarily decided that a nucleotide was to be included in the consensus only if it was present in at least 50% of all the sequences analyzed. If two nucleotides, each represented at less than 50%, gave a summed total of at least 75% representation for a single position, then both are shown in brackets. Key: -in the Distance from +1 to ATG (bases) means that the authors had not determined the +1 position 
The reason why the methionine start codon (ATG) is not 100% perfectly conserved within the Kozak consensus is that, for reasons unknown, the gene frq (Ref 33) starts its protein sequence with a valine (GTT). 
It is also interesting to note that the choice of the second codon appears to be limited in that about half of the second codons have a guanosine in the first position and another half have a cytosine in the second position. 
On the whole, our consensus shows a good resemblance to the mammalian Kozak sequence with a similar hierarchy of nucleotide preference for a given position, although the degree of preference may be shifted. An exception is the nucleotide position immediately preceding the initiator methionine codon (ATG) where N. crassa exhibits a definite suppression of thymine in contrast to a positive preference for any other nucleotide. 
Fifty genes among the 77 analyzed have a determined mRNA 5' end. When several 5' ends were presented, +1 was taken to be the most distal from the ATG except when given by the authors themselves. In this way the mRNA sequences before the ATG have lengths between 30 and 622 bases. 
The stop codon, determined by computer analysis by the authors, TAA in 62% of the cases, TGA in 27% and TAG in 11% 

Table I . Consensus for initiation of translation and stop codons in Neurospora crassa

 I 
	73	15 68	cmt trp-3	127 147	TCTATCAAAATGGGT TCATACACAATGGAG	TAA TAA
	17 74	16 69	con-8 Ubi	221 -	ACAATAACCATGGAT ACCCCCATCATGCAG	TGA TAA
	18 75	17 70	con-10 ucr	91 -	ATCGTCAACATGGCT ACCGACACAATGGCG	TAG TAA
	19 76	18 71	con-13 vma-1	86 -	CGTCGCAAGATGCCC TCGCCCAAGATGGCT	TGA TGA
	20 77	19 72	cot-1 vma-2	--	GGTACCAAGATGGAC TCTTCCACAATGGCC	TAA TAA
	21	20	cpc-1	622	TCCATCAAGATGCGT	TAA
	22	21	cpi	-	TTAGTGAAAATGTTT	TAA
	23	22	crp-1	-	GCAGACAACATGGTA	TAA
	24	23	crp-2	62	ACCGTCAAGATGCCC	TGA
	25	24	crp-3	58	GCCGGCAAAATGGGT	TAA
	26	25	cya-4	146	GCCGCCACCATGCTT	TAA
	27	26	cys-3	30	CATGGCACAATGTCT	TAA
	28	27	cys-14	32	GACACTCAGATGGCT	TAA
	29	28	cyt-2	-	TCAGTCGCAATGGGT	TAA
	30	29	cyt-18	-	TCACATCAAATGCTG	TAA
	31	30	cyt-20	57	GTCCTCTGGATGCCG	TAA
	32	31	cyt-21	125	CGGTCCAACATGGTT	TGA
	33	32	for	66	TCAGTCACCATGTCT	TAA
	34	33	frq	-	GAAACCTGAGTTGGA	TGA
	35	34	grg-1	89	TCAACCAAAATGGAT	TAA
	36	35	H3	-	ACCATCACAATGGCC	TAA
	37	35	H4	-	CATATCAAAATGACT	TAA
	38	36	his-3	124	GAAAACACCATGGAG	TAA
	39	37	hsp30	120	AAGTCAAAAATGGCG	TAA
	40	38	ilv-2	-	TCCATCACAATGGCC	TAA
	41	39	laccase	190	TTTATCACCATGAAA	TAG
	42	40	leu-5	146	CACAACGCGATGCCT	TAG
	43	41	leu-6	220	TAAACAAACATGGCC	TAA
	44	42	lox	123	TCATACAAGATGAAG	TGA
	45	43	met-7	98	ATCACAGCCATGCTT	TGA
	46	44	mrp-3	-	CCTCTCACCATGATC	TAA
	47	45	mta-1	-	ACCGAAACAATGGAC	TGA
	48	46	mtA-1	-	AGAAACACGATGTCG	TAG
	49	47	nac	162	CCGGTGACAATGACG	TAA
	50	48	ncypt1	-	TTGCCCATCATGAAC	TAA
	51	49	nit-2	284	TGTGCGACAATGGCG	TAA
	52	50	nit-3	110	AGCATCATCATGGAG	TGA
	53	51	nit-4	39	CCCCGGCAGATGAAC	TGA
	54	52	nuc-1	-	GCGGGCGTGATGAAC	TAA
	No. Ref. 55 53	Gene Distance from +1 nur22 -	Kozak Sequence ACCGTCAAGATGGCG	Stop codon TGA
	56	54	nur40	to ATG (bases) -	ACTCACAAGATGGCT	TGA
	57	55	nur49	-	Consensus:CNNNCAATGGC CAAACAACAATGGCG	TAA
	1 58	1 56	acp pho-4	46 145	AATATCACAATGGCG TCGTTCAAGATGGTT	TAA TGA
	2 59 57+58 2	acu-3 pma-1	-56	CTGCCCATCATGGCT ATAACGCCAATGGCG	TAG TAA
	3 60	3 59	acu-5 preg	103 -	ATACGAGTTATGGCG GGATTTGTGATGCTG	TAA TAA
	4 61	4 60	acu-8 pyr-4	-61	TCACCAACCATGGCG ACAGCCAACATGTCG	TAA TAG
	5 62	5 61	acu-9 qa-1F	60 330	CTTTTCACAATGGCT AATCCCAACATGCCG	TAA TAG
	6 63 61+62 6	al-1 qa-1S	-346	ACAGACAAAATGGCT GCCGCCATCATGAAC	TAG TGA
	7 64	7 61	al-3 qa-2	90 85	CACGTCACCATGGCC CCAAACACAATGGCG	TGA TGA
	8 65	8 61	alc qa-3	54 83	TCCCTCACCATGACC TATATCACCATGTCG	TAA TGA
	9 66 61+63 9	am qa-4	109 190	ACCTTCAAAATGTCT CCTTTCGCCATGCCG	TAA TAA
	10 67	10 61	arg-2 qa-x	118 84	CAAGTCAAGATGTTC TCAGCAGCCATGACA	TAA TGA
	11 68	11 61	atp-1 qa-y	90 133	CTCCACAACATGTTC CGCGTCAAGATGACT	TAA TAA
	12 69	11 64	atp-2 sod-1	58 -	ATCGTCAAGATGTTC TCCGTCAAAATGGTC	TAA TAA
	13 70	12 65	bli-7 spe-1	110 535	ACCGCCAAAATGCAG TCTTGGGATATGGTT	TAA TAA
	14 71	13 66	Bml T	-94	ACCGTCAAGATGCGT GCAGCAACCATGAGC	TAA TGA
	15 72	14 67	chs-1 trp-1	69 29	TCCGCAACCATGGCG CCAATCACAATGTCG	TGA TAA

Bruchez et al.: Regulatory sequences involved in the translation of Neurospora cr Published by New Prairie Press, 2017 

Fungal Genetics Reports, Vol.40 [1993], Art. 3 https://newprairiepress.org/fgr/vol40/iss1/3 DOI: 10.4148/1941-4765.1394 

Bruchez et al.: Regulatory sequences involved in the translation of Neurospora cr Published by New Prairie Press, 2017
J J P Bruchez, J Eberle, V E . A Russo
Regulatory sequences involved in the translation of Neurospora crassa mRNA: Kozak sequences and stop codons