Codon bias of IPI gene in leguminous plants

doi:10.3969/j.issn.1004-1524.2022.06.02

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (6): 1114-1123.DOI: 10.3969/j.issn.1004-1524.2022.06.02

• Crop Science • Previous Articles Next Articles

Codon bias of IPI gene in leguminous plants

JIANG Ruiping(), ZHAO Chenhui, LI Wenjie, AN Qiuju, LI Jialun, ZHOU Jiayu, LI Suiyan, LIAO Hai()

School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China

Received:2021-08-30 Online:2022-06-25 Published:2022-06-30
Contact: LIAO Hai

Abstract

Abstract:

Isopentenyl diphosphate isomerases (IPI), as a key enzyme in 2-C-methyl-D-erythritol 4-phosphate (MEP) and Mevalonate (MVA) pathways, takes part in the biosynthesis of terpenoids. Since leguminous species contain a variety of terpenoids, the codon bias of IPI genes from leguminous species will provide significant basis to increase those expressing levels and thus the terpenoids contents in leguminous species. In this study, Codon W, EMBOSS, ENc-GC3s and PR2-plot were used to calculate the base composition, relative synonymous codon usage (RSCU), effective number of codons (ENc), codon adaptation index (CAI), and etc. As a result, 7 codons showed strong preference (RSCU >1), in which GGU was the most optimal codon. That the low contents (<0.5) of both GC (GC content) and GC3s (GC content of the third base) indicated that A/U was preferable terminal codon. The low expressing level of IPI genes was probably due to the Enc values ranging from 46.69 to 55 and the CAI values ranging from 0.23 to 0.27. The results of ENc-GC3s and PR2-plot supported that the formation of codon bias was mainly contributed from natural selection. Compared with RSCU clustering, the phylogenetic tree based on CDS was closer to the result of classification based on morphology. Finally, Escherichia coli, Nicotiana tabacum and Arabidopsis thaliana were proposed to be suitable hosts for IPI genes from leguminous species. Therefore, the result of this paper laid foundation for transformation of codons and genetic engineering of IPI genes.

Key words: codon usage bias, cluster analysis, isopentenyl diphosphate isomerases, leguminous plants

CLC Number:

JIANG Ruiping, ZHAO Chenhui, LI Wenjie, AN Qiuju, LI Jialun, ZHOU Jiayu, LI Suiyan, LIAO Hai. Codon bias of IPI gene in leguminous plants[J]. Acta Agriculturae Zhejiangensis, 2022, 34(6): 1114-1123.

Figures/Tables 7

References 30

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物种Species	登录号Accession number	ENc	CAI	GC3s	GC
决明Cassia obtusifolia	SRP144670	50.107	0.230	0.421	0.46
相思子Abrus precatorius	XM_027497746.1	50.245	0.250	0.433	0.461
蔓花生Arachis duranensis	XM_016106509.2	46.691	0.265	0.492	0.478
落花生1 Arachis hypogaea1	XM_025840579.2	46.797	0.266	0.492	0.479
落花生2 Arachis hypogaea2	XM_025793828.2	46.726	0.270	0.503	0.481
木豆Cajanus cajan	XM_020364407.2	50.705	0.249	0.490	0.482
鹰嘴豆Cicer arietinum	XM_004492783.3	50.049	0.246	0.444	0.452
大豆1 Glycine max1	XM_003534463.4	50.437	0.253	0.482	0.473
大豆2 Glycine max2	NM_001255206.3	49.83	0.272	0.479	0.473
野大豆1 Glycine soja1	XM_028358779.1	49.324	0.268	0.479	0.474
野大豆2 Glycine soja2	XM_028391951.1	50.437	0.253	0.482	0.473
狭叶羽扇豆1 Lupinus angustifolius1	XM_019575678.1	50.768	0.249	0.420	0.444
狭叶羽扇豆2 Lupinus angustifolius2	XM_019594813.1	50.273	0.263	0.420	0.442
狭叶羽扇豆3 Lupinus angustifolius3	XM_019575969.1	49.93	0.266	0.419	0.444
狭叶羽扇豆4 Lupinus angustifolius4	XM_019571013.1	49.969	0.266	0.420	0.444
狭叶羽扇豆5 Lupinus angustifolius5	XM_019559793.1	51.774	0.272	0.432	0.447
狭叶羽扇豆6 Lupinus angustifolius6	XM_019584336.1	50.084	0.270	0.423	0.445
紫苜蓿Medicago sativa	JF510483.1	51.110	0.258	0.437	0.464
蒺藜苜蓿Medicago truncatula	XM_003624130.4	50.437	0.253	0.482	0.473
阿根廷牧豆树Prosopis alba	XM_028934525.1	52.856	0.232	0.482	0.482
葛Pueraria lobata	AY315650.1	51.672	0.248	0.483	0.475
赤豆Vigna angularis	XM_017563749.1	54.405	0.268	0.482	0.472
绿豆Vigna radiata	XM_014642829.2	51.829	0.260	0.478	0.474
豇豆Vigna unguiculata	XM_028072473.1	55.000	0.245	0.488	0.475
膜荚黄芪Astragalus membranaceus	KF355965.1	52.678	0.235	0.416	0.437
日本杜鹃Rhododendron japonicum	LC021366.1	53.610	0.258	0.462	0.461
小粒咖啡Coffea arabica	XM_027231362.1	51.660	0.245	0.46	0.463
长春花Catharanthus roseus	EU135981.1	51.610	0.247	0.468	0.452
木槿Hibiscus syriacus	XM_039183691.1	57.890	0.215	0.457	0.468
胡桃Juglans regia	XM_041143473.1	53.600	0.222	0.436	0.466
烟草Nicotiana tabacum	XM_016633077.1	54.579	0.259	0.424	0.443
拟南芥Arabidopsis thaliana	NM_111146.4	53.079	0.239	0.402	0.440

物种Species	登录号Accession number	ENc	CAI	GC3s	GC
决明Cassia obtusifolia	SRP144670	50.107	0.230	0.421	0.46
相思子Abrus precatorius	XM_027497746.1	50.245	0.250	0.433	0.461
蔓花生Arachis duranensis	XM_016106509.2	46.691	0.265	0.492	0.478
落花生1 Arachis hypogaea1	XM_025840579.2	46.797	0.266	0.492	0.479
落花生2 Arachis hypogaea2	XM_025793828.2	46.726	0.270	0.503	0.481
木豆Cajanus cajan	XM_020364407.2	50.705	0.249	0.490	0.482
鹰嘴豆Cicer arietinum	XM_004492783.3	50.049	0.246	0.444	0.452
大豆1 Glycine max1	XM_003534463.4	50.437	0.253	0.482	0.473
大豆2 Glycine max2	NM_001255206.3	49.83	0.272	0.479	0.473
野大豆1 Glycine soja1	XM_028358779.1	49.324	0.268	0.479	0.474
野大豆2 Glycine soja2	XM_028391951.1	50.437	0.253	0.482	0.473
狭叶羽扇豆1 Lupinus angustifolius1	XM_019575678.1	50.768	0.249	0.420	0.444
狭叶羽扇豆2 Lupinus angustifolius2	XM_019594813.1	50.273	0.263	0.420	0.442
狭叶羽扇豆3 Lupinus angustifolius3	XM_019575969.1	49.93	0.266	0.419	0.444
狭叶羽扇豆4 Lupinus angustifolius4	XM_019571013.1	49.969	0.266	0.420	0.444
狭叶羽扇豆5 Lupinus angustifolius5	XM_019559793.1	51.774	0.272	0.432	0.447
狭叶羽扇豆6 Lupinus angustifolius6	XM_019584336.1	50.084	0.270	0.423	0.445
紫苜蓿Medicago sativa	JF510483.1	51.110	0.258	0.437	0.464
蒺藜苜蓿Medicago truncatula	XM_003624130.4	50.437	0.253	0.482	0.473
阿根廷牧豆树Prosopis alba	XM_028934525.1	52.856	0.232	0.482	0.482
葛Pueraria lobata	AY315650.1	51.672	0.248	0.483	0.475
赤豆Vigna angularis	XM_017563749.1	54.405	0.268	0.482	0.472
绿豆Vigna radiata	XM_014642829.2	51.829	0.260	0.478	0.474
豇豆Vigna unguiculata	XM_028072473.1	55.000	0.245	0.488	0.475
膜荚黄芪Astragalus membranaceus	KF355965.1	52.678	0.235	0.416	0.437
日本杜鹃Rhododendron japonicum	LC021366.1	53.610	0.258	0.462	0.461
小粒咖啡Coffea arabica	XM_027231362.1	51.660	0.245	0.46	0.463
长春花Catharanthus roseus	EU135981.1	51.610	0.247	0.468	0.452
木槿Hibiscus syriacus	XM_039183691.1	57.890	0.215	0.457	0.468
胡桃Juglans regia	XM_041143473.1	53.600	0.222	0.436	0.466
烟草Nicotiana tabacum	XM_016633077.1	54.579	0.259	0.424	0.443
拟南芥Arabidopsis thaliana	NM_111146.4	53.079	0.239	0.402	0.440

氨基酸 Amino acid	密码子 Codon	RSCU_high	RSCUl_ow	ΔRSCU	氨基酸 Amino acid	密码子 Codon	RSCU_high	RSCU_low	ΔRSCU
苯丙氨酸 Phenylalanine	UUU	0.648	0.202	0.446	酪氨酸 Tyrosine	UAU	1.056	1	0.056
苯丙氨酸 Phenylalanine	UUC	1.352	1.798	-0.446	酪氨酸 Tyrosine	UAC	0.944	1	-0.056
亮氨酸 Leucine	UUA	0.184	0	0.184	终止密码 Terminal codon	UAA	3	3	0
	UUG	1.456	1.986	-0.530	终止密码 Terminal codon	UAG	0	0	0
	CUU	1.388	1.898	-0.510	组氨酸 Histidine	CAU	1.080	1.170	-0.090
	CUC	0.856	0.804	0.052	组氨酸 Histidine	CAC	0.920	0.830	0.090
	CUA	0.262	0.154	0.108	谷氨酰胺 Glutarnine	CAA	0.500	0.460	0.040
	CUG***	1.850	1.152	0.698	谷氨酰胺 Glutarnine	CAG	1.500	1.540	-0.04
异亮氨酸 Isoleucine	AUU*	2.016	1.888	0.128	天冬酰胺 Asparagine	AAU	1.252	0.838	0.414
	AUC	0.698	0.938	-0.240	天冬酰胺 Asparagine	AAC	0.748	1.162	-0.414
	AUA	0.288	0.174	0.114	赖氨酸 Lysine	AAA	0.840	0.832	0.008
甲硫氨酸 Methionine	AUG	1	1	0	赖氨酸 Lysine	AAG	1.16	1.172	-0.012
缬氨酸 Valine	GUU	1.108	1.426	-0.318	天冬氨酸 Asparticacid	GAU*	1.284	1.200	0.084
	GUC	0.574	0.646	-0.072	天冬氨酸 Asparticacid	GAC	0.716	0.800	-0.084
	GUA	0.702	0.576	0.126	谷氨酸 Glutamicacid	GAA	0.958	1.004	-0.046
	GUG**	1.612	1.354	0.258	谷氨酸 Glutamicacid	GAG	1.042	0.996	0.046
丝氨酸 Serine	UCU	2.478	3.766	-1.288	半胱氨酸 Cystine	UGU	0.872	0.740	0.132
	UCC*	1.234	1.118	0.116	半胱氨酸 Cystine	UGC	1.128	1.260	-0.132
	UCA	0.920	0.094	0.826	终止密码 Terminal codon	UGA	0	0	0
	UCG	0.208	0.374	-0.166	终止密码 Terminal codon
脯氨酸 Proline	CCU	2.140	2.468	-0.328	色氨酸 Tryptophan	UGG	1	1	0
	CCC	0.536	0.268	0.268	精氨酸 Arginine	CGU	0.902	0.920	-0.018
	CCA	1.326	1.264	0.062		CGC**	1.590	1.382	0.208
	CCG	0	0	0		CGA	0.622	0.494	0.128
苏氨酸 Threonine	ACU	0.844	1.134	-0.290		CGG	0.170	0.146	0.024
	ACC	1.562	1.614	-0.052	丝氨酸 Serine	AGU	0.476	0.282	0.194
	ACA	1.386	0.908	0.478	丝氨酸 Serine	AGC	0.684	0.374	0.310
	ACG	0.208	0.342	-0.134	精氨酸 Arginine	AGA*	1.744	1.602	0.142
丙氨酸 Alanine	GCU	1.462	1.746	-0.284	精氨酸 Arginine	AGG	0.974	1.458	-0.484
	GCC	1.248	1.468	-0.22	甘氨酸 Glycine	GGU***	2.074	1.132	0.942
	GCA	1.048	0.514	0.534		GGC	0.506	1.226	-0.72
	GCG	0.240	0.266	-0.026		GGA	1.274	1.518	-0.244
						GGG	0.146	0.124	0.022

氨基酸 Amino acid	密码子 Codon	RSCU_high	RSCUl_ow	ΔRSCU	氨基酸 Amino acid	密码子 Codon	RSCU_high	RSCU_low	ΔRSCU
苯丙氨酸 Phenylalanine	UUU	0.648	0.202	0.446	酪氨酸 Tyrosine	UAU	1.056	1	0.056
苯丙氨酸 Phenylalanine	UUC	1.352	1.798	-0.446	酪氨酸 Tyrosine	UAC	0.944	1	-0.056
亮氨酸 Leucine	UUA	0.184	0	0.184	终止密码 Terminal codon	UAA	3	3	0
	UUG	1.456	1.986	-0.530	终止密码 Terminal codon	UAG	0	0	0
	CUU	1.388	1.898	-0.510	组氨酸 Histidine	CAU	1.080	1.170	-0.090
	CUC	0.856	0.804	0.052	组氨酸 Histidine	CAC	0.920	0.830	0.090
	CUA	0.262	0.154	0.108	谷氨酰胺 Glutarnine	CAA	0.500	0.460	0.040
	CUG***	1.850	1.152	0.698	谷氨酰胺 Glutarnine	CAG	1.500	1.540	-0.04
异亮氨酸 Isoleucine	AUU*	2.016	1.888	0.128	天冬酰胺 Asparagine	AAU	1.252	0.838	0.414
	AUC	0.698	0.938	-0.240	天冬酰胺 Asparagine	AAC	0.748	1.162	-0.414
	AUA	0.288	0.174	0.114	赖氨酸 Lysine	AAA	0.840	0.832	0.008
甲硫氨酸 Methionine	AUG	1	1	0	赖氨酸 Lysine	AAG	1.16	1.172	-0.012
缬氨酸 Valine	GUU	1.108	1.426	-0.318	天冬氨酸 Asparticacid	GAU*	1.284	1.200	0.084
	GUC	0.574	0.646	-0.072	天冬氨酸 Asparticacid	GAC	0.716	0.800	-0.084
	GUA	0.702	0.576	0.126	谷氨酸 Glutamicacid	GAA	0.958	1.004	-0.046
	GUG**	1.612	1.354	0.258	谷氨酸 Glutamicacid	GAG	1.042	0.996	0.046
丝氨酸 Serine	UCU	2.478	3.766	-1.288	半胱氨酸 Cystine	UGU	0.872	0.740	0.132
	UCC*	1.234	1.118	0.116	半胱氨酸 Cystine	UGC	1.128	1.260	-0.132
	UCA	0.920	0.094	0.826	终止密码 Terminal codon	UGA	0	0	0
	UCG	0.208	0.374	-0.166	终止密码 Terminal codon
脯氨酸 Proline	CCU	2.140	2.468	-0.328	色氨酸 Tryptophan	UGG	1	1	0
	CCC	0.536	0.268	0.268	精氨酸 Arginine	CGU	0.902	0.920	-0.018
	CCA	1.326	1.264	0.062		CGC**	1.590	1.382	0.208
	CCG	0	0	0		CGA	0.622	0.494	0.128
苏氨酸 Threonine	ACU	0.844	1.134	-0.290		CGG	0.170	0.146	0.024
	ACC	1.562	1.614	-0.052	丝氨酸 Serine	AGU	0.476	0.282	0.194
	ACA	1.386	0.908	0.478	丝氨酸 Serine	AGC	0.684	0.374	0.310
	ACG	0.208	0.342	-0.134	精氨酸 Arginine	AGA*	1.744	1.602	0.142
丙氨酸 Alanine	GCU	1.462	1.746	-0.284	精氨酸 Arginine	AGG	0.974	1.458	-0.484
	GCC	1.248	1.468	-0.22	甘氨酸 Glycine	GGU***	2.074	1.132	0.942
	GCA	1.048	0.514	0.534		GGC	0.506	1.226	-0.72
	GCG	0.240	0.266	-0.026		GGA	1.274	1.518	-0.244
						GGG	0.146	0.124	0.022

Codon bias of IPI gene in leguminous plants

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