Amendments may be proposed by the City Council; by the Planning Commission; or by any resident of, owner of, optionee of, or lessee of property in the City, but only in the manner and pursuant to the procedure set forth in Section 1139.03. When the City Council proposes an amendment, it shall transmit its proposal to the Planning Commission, for the report required by Sections 1139.05 to 1139.07, of this Zoning Code.